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1
NOVEL NUCLEIC ACIDS AND POLYPEPTIDES
1. CROSS REFERENCE TO RELATED APPLICATIONS
This application claims the priority benefit of U.S. Provisional Application
Serial No.
60/416,186 filed October 2, 2002 entitled "Novel Nucleic Acids and
Polypeptides" , which
contains material previously disclosed in the following applications: U.S.
Application Serial
No. 10/084,643 filed February 26, 2002 entitled "Novel Nucleic Acids and
Polypeptides",
Attorney Docket No. 21272-502; PCT Application Serial No. PCT/US00/35017 filed
December 22, 2000 entitled "Novel Contigs Obtained from Various Libraries",
Attorney
Docket No. 784CIP3A/PCT; PCT Application Serial No. PCT/LTSO1/02623 filed
January 25,
2001 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket
No.
785CIP3/PCT; PCT Application Serial No. PCT/LTSO1/03800 filed February 5, 2001
entitled
"Novel Contigs Obtained from Various Libraries", Attorney Docket No.
787CIP3/PCT; PCT
Application Serial No. PCT/USO1/04927 filed February 26, 2001 entitled "Novel
Contigs
Obtained from Various Libraries", Attorney Docket No. 788CIP3/PCT; PCT
Application
Serial No. PCT/USO1/04941 filed March 5, 2001 entitled "Novel Contigs Obtained
from
Various Libraries", Attorney Docket No. 789CIP3/PCT; PCT Application Serial
No.
PCT/LTSO1/08631 filed March 30, 2001 entitled "Novel Contigs Obtained from
Various
Libraries", Attorney Docket No. 790CIP3/PCT; PCT Application Serial No.
PCT/LTSO1/08656 filed April 18, 2001 entitled "Novel Contigs Obtained from
Various
Libraries", Attorney Docket No. 791 CIP3/PCT; all of which are incorporated
herein by
reference in their entirety.
2. DACKGROUND OF THE INVENTION
2.1 TECHNICAL FIELD
The present invention provides novel polynucleotides and proteins encoded by
such
polynucleotides, along with uses for these polynucleotides and proteins, for
example in
therapeutic, diagnostic and research methods.
2.2 BACKGROUND
Technology aimed at the discovery of protein factors (including e.g.,
cytokines, such
as lymphokines, interferons, circulating soluble factors, chemokines, and
interleukins) has
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2
matured rapidly over the past decade. The now routine hybridization cloning
and expression
cloning techniques clone novel polynucleotides "directly" in the sense that
they rely on
information directly related to the discovered protein (i.e., partial
DNA/amino acid sequence
of the protein in the case of hybridization cloning; activity of the protein
in the case of
expression cloning). More recent "indirect" cloning techniques such as signal
sequence
cloning, which isolates DNA sequences based on the presence of a now well-
recognized
secretory leader sequence motif, as well as various PCR-based or low
stringency
hybridization-based cloning techniques, have advanced the state of the art by
making
available large numbers of DNA/amino acid sequences for proteins that are
known to have
biological activity, for example, by virtue of their secreted nature in the
case of leader
sequence cloning, by virtue of their cell or tissue source in the case of PCR-
based
techniques, or by virtue of structural similarity to other genes of known
biological activity.
Identified polynucleotide and polypeptide sequences have numerous applications
in,
for example, diagnostics, forensics, gene mapping; identification of mutations
responsible
for genetic disorders or other traits, to assess biodiversity, and to produce
many other types
of data and products dependent on DNA and amino acid sequences.
3. SU ~Y ~F" TIIE I1~TVE1~TTIOIV
The compositions of the present invention include novel isolated polypeptides,
novel
isolated polynucleotides encoding such polypeptides, including recombinant DNA
molecules,
cloned genes or degenerate variants thereof, especially naturally occurring
variants such as
allelic variants, antisense polynucleotide molecules, and antibodies that
specifically recognize
one or more epitopes present on such polypeptides, as well as hybridomas
producing such
antibodies.
The compositions of the present invention additionally include vectors,
including
expression vectors, containing the polynucleotides of the invention, cells
genetically engineered
to contain such polynucleotides and cells genetically engineered to express
such
polynucleotides.
The present invention relates to a collection or library of at least one novel
nucleic acid
sequence assembled from expressed sequence tags (ESTs) isolated mainly by
sequencing by
hybridization (SBH), and in some cases, sequences obtained from one or more
public
databases. 'The invention relates also to the proteins encoded by such
polynucleotides, along
with therapeutic, diagnostic and research utilities for these polynucleotides
and proteins. These
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nucleic acid sequences are designated as SEQ ID NO: 1-684, or 1369-1966 and
are provided in
the Sequence Listing. In the nucleic acids provided in the Sequence Listing, A
is adenine; C is
cytosine; G is guanine; T is thymine; and N is any of the four bases or
unknown. In the amino
acids provided in the Sequence Listing, an asterisk (*) corresponds to the
stop codon.
The nucleic acid sequences of the present invention also include, nucleic acid
sequences
that hybridize to the complement of SEQ ID NO: 1-684, or 1369-1966 under
stringent
hybridization conditions; nucleic acid sequences which are allelic variants or
species
homologues of any of the nucleic acid sequences recited above, or nucleic acid
sequences that
encode a peptide comprising a specific domain or truncation of the peptides
encoded by SEQ
ZD NO: 1-684, or 1369-1966. A polynucleotide comprising a nucleotide sequence
having at
least 90°!o identity to an identifying sequence of SEQ ID NO: 1-684, or
1369-1966 or a
degenerate variant or fragment thereof. The identifying sequence can be 100
base pairs in
length.
The nucleic acid sequences of the present invention also include the sequence
information from the nucleic acid sequences of SEQ Ilk NO: 1-684, or 1369-
1966. The
sequence information can be a segment of any one of SEQ 11? NO: 1-684, or 1369-
1966 that
uniquely identifies or represents the sequence information of SEQ 11? NO: 1-
684, or 1369-1966.
A collection as used in this application can be a collection of only one
polynucleotide.
The collection of sequence information or identifying information of each
sequence can be
provided on a nucleic acid array. In one embodiment, segments of sequence
information are
provided on a nucleic acid array to detect the polynucleotide that contains
the segment. The
array can be designed to detect full-match or mismatch to the polynucleotide
that contains the
segment. 'The collection can also be provided in a computer-readable format.
This invention also includes the reverse or direct complement of any of the
nucleic acid
sequences recited above; cloning or expression vectors containing the nucleic
acid sequences;
and host cells or organisms transformed with these expression vectors. Nucleic
acid sequences
(or their reverse or direct complements) according to the invention have
numerous applications
in a variety of techniques known to those skilled in the art of molecular
biology, such as use as
hybridization probes, use as primers for PCR, use in an array, use in computer-
readable media,
use in sequencing full-length genes, use for chromosome and gene mapping, use
in the
recombinant production of protein, and use in the generation of anti-sense DNA
or RNA, their
chemical analogs and the like.
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4
In a preferred embodiment, the nucleic acid sequences of SEQ ID NO: 1-684, or
1369-
1966 or novel segments or parts of the nucleic acids of the invention are used
as primers in
expression assays that are well known in the art. In a particularly preferred
embodiment, the
nucleic acid sequences of SEQ ff~ NO: 1-684, or 1369-1966 or novel segments or
parts of the
nucleic acids provided herein are used in diagnostics for identifying
expressed genes or, as well
known in the art and exemplified by Vollrath et al., Science 258:52-59 (1992),
as expressed
sequence tags for physical mapping of the human genome.
The isolated polynucleotides of the invention include, but are not limited to,
a
polynucleotide comprising any one of the nucleotide sequences set forth in SEQ
ZD NO: 1-684,
or 1369-1966; a polynucleotide comprising any of the full length protein
coding sequences of
SEQ ~ NO: 1-684, or 1369-1966; and a polynucleotide comprising any of the
nucleotide
sequences of the mature protein coding sequences of SEQ ID NO: 1-684, or 1369-
1966. The
polynucleotides of the present invention also include, but are not limited to,
a polynucleotide
that hybridizes under stringent hybridization conditions to (a) the complement
of any one of the
nucleotide sequences set forth in SEQ ID NO: 1-684, or 1369-1966; (b) a
nucleotide sequence
encoding any one of the amino acid sequences set forth in SEQ 11? NO: 1-684,
or 1369-1966;
(c) a polynuclcotidc which is an allelic variant of any polynuclcotides
recited above; (d) a
polynucleotide which encodes a species homologue (e.g. orthologs) of any of
the proteins
recited above; or (e) a polynucleotide that encodes a polypeptide comprising a
specific domain
or truncation of any of the polypeptides comprising an amino acid sequence set
forth in SEQ ID
NO: 685-1368, or 1967-2564, or Tables 3A., 3B, 5, 7, or 8.
'1 he isolated polypeptides of the invention include, but are not limited to,
a polypeptide
comprising any of the amino acid sequences set forth in the Sequence Listing;
or the
corresponding full length or mature protein. Polypeptides of the invention
also include
polypeptides with biological activity that are encoded by (a) any of the
polynucleotides having
a nucleotide sequence set forth in SEQ 11? NO: 1-684, or 1369-1966; or (b)
polynucleotides that
hybridize to the complement of the polynucleotides of (a) under stringent
hybridization
conditions. Biologically active variants of any ofthe polypeptide sequences in
the Sequence
Listing, and "substantial equivalents" thereof (e.g., with at least about 65%,
70%, 75%, 80%,
85%, 90%, 95%, 98% or 99% amino acid sequence identity) that preferably retain
biological
activity are also contemplated. The polypeptides of the invention may be
wholly or partially
chemically synthesized but are preferably produced by recombinant means using
the genetically
engineered cells (e.g. host cells) of the invention.
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The invention also provides compositions comprising a polypeptide of the
invention.
Polypeptide compositions of the invention may further comprise an acceptable
carrier, such
as a hydrophilic, e.g., pharmaceutically acceptable, carrier.
The invention also provides host cells transformed or transfected with a
polynucleotide of the invention.
The invention also relates to methods for producing a polypeptide of the
invention
comprising growing a culture of the host cells of the invention in a suitable
culture medium
under conditions permitting expression of the desired polypeptide, and
purifying the
polypeptide from the culture or from the host cells. Preferred embodiments
include those in
which the protein produced by such processes is a mature form of the protein.
Polynucleotides according to the invention have numerous applications in a
variety
of techniques known to those skilled in the art of molecular biology. These
techniques
include use as hybridization probes, use as oligomers, or primers, for PCR,
use for
chromosome and gene mapping, use in the recombinant production of protein, and
use in
generation of anti-sense DNA or RNA, their chemical analogs and the like. For
example,
when the expression of an mRNA is largely restricted to a particular cell or
tissue type9
polynucleotides of the invention can be used as hybridization probes to detect
the presence
of the particular cell or tissue mRNA in a sample using, e.~., in. situ
hybridization.
In other exemplary embodiments, the polynucleotides are used in diagnostics as
expressed sequence tags for identifying expressed genes or, as well known in
the art and
ey~emplif'md by ~ollrath et al., Science 258:52-5~ ~1~~2), as expressed
sequence tags for
physical mapping of the human genome.
The polypeptides according to the invention can be used in a variety of
conventional
procedures and methods that are currently applied to other proteins. For
example, a
polypeptide of the invention can be used to generate an antibody that
specifically binds the
polypeptide. Such antibodies, particularly monoclonal antibodies, are useful
for detecting or
quantitating the polypeptide in tissue. The polypeptides of the invention can
also be used as
molecular weight markers, and as a food supplement.
Methods are also provided for preventing, treating, or ameliorating a medical
condition which comprises the step of administering to a mammalian subject a
therapeutically effective amount of a composition comprising a polypeptide of
the present
invention and a pharmaceutically acceptable Garner.
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In particular, the polypeptides and polynucleotides of the invention can be
utilized,
for example, in methods for the prevention and/or treatment of disorders
involving aberrant
protein expression or biological activity.
The present invention further relates to methods for detecting the presence of
the
polynucleotides or polypeptides of the invention in a sample. Such methods
can, for
example, be utilized as part of prognostic and diagnostic evaluation of
disorders as recited
herein and for the identification of subjects exhibiting a predisposition to
such conditions.
The invention provides a method for detecting the polynucleotides of the
invention in a
sample, comprising contacting the sample with a compound that binds to and
forms a
complex with the polynucleotide of interest for a period sufficient to form
the complex and
under conditions sufficient to form a complex and detecting the complex such
that if a
complex is detected, the polynucleotide of interest is detected. The invention
also provides a
method for detecting the polypeptides of the invention in a sample comprising
contacting the
sample with a compound that binds to and forms a complex with the polypeptide
under
conditions and for a period sufficient to form the complex and detecting the
formation of the
complex such that if a complex is formed, the polypeptide is detected.
The invention also provides kits comprising polynucleotide probes and/or
monoclonal antibodies, and optionally quantitative standards, for carrying out
methods of the
invention. Furthermore, the invention provides methods for evaluating the
efficacy of drugs,
and monitoring the progress of patients, involved in clinical trials for the
treatment of
disorders as recited above.
The invention also provides methods for the identification of compounds that
modulate (i.e., increase or decrease) the expression or activity of the
polynucleotides andJor
polypeptides of the invention. Such methods can be utilized, for example, for
the
identification of compounds that can ameliorate symptoms of disorders as
recited herein.
Such methods can include, but are not limited to, assays for identifying
compounds and
other substances that interact with (e.g., bind to) the polypeptides of the
invention. The
invention provides a method for identifying a compound that binds to the
polypeptides of the
invention comprising contacting the compound with a polypeptide of the
invention in a cell
for a time sufficient to form a polypeptide/compound complex, wherein the
complex drives
expression of a reporter gene sequence in the cell; and detecting the complex
by detecting
the reporter gene sequence expression such that if expression of the reporter
gene is detected
the compound that binds to a polypeptide of the invention is identified.
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7
The methods of the invention also provide methods for treatment which involve
the
administration of the polynucleotides or polypeptides of the invention to
individuals
exhibiting symptoms or tendencies. In addition, the invention encompasses
methods for
treating diseases or disorders as recited herein comprising administering
compounds and
other substances that modulate the overall activity of the target gene
products. Compounds
and other substances can affect such modulation either on the level of target
gene/protein
expression or target protein activity.
The polypeptides of the present invention and the polynucleotides encoding
them are
also useful for the same functions known to one of skill in the art as the
polypeptides and
polynucleotides to which they have homology (set forth in Tables 2A and 2B);
for which
they have a signature region (as set forth in Tables 3A and 3B); or for which
they have
homology to a gene family (as set forth in Tables 4A and 4B). If no homology
is set forth
for a sequence, then the polypeptides and polynucleotides of the present
invention are useful
for a variety of applications, as described herein, including use in arrays
for detection.
4. DETAIIdEII I)E~CI~I~TI~I~T ~~ TII~TI~TTI~l~
4.1 DEFIIVITI~l~S
It must be noted that as used herein and in the appended claims, the singular
forms
"a", "an" and "the" include plural references unless the context clearly
dictates otherwise.
The term "active" refers t~ th~se f~rms of the polypept~ade which retain the
biol~gic
and/~r immunologic activities of any naturally occurriaig polypeptide.
According t~ the
inventi~n, the terms "biologically active" or "biological activity" refer t~ a
protein or peptide
having structural, regulatory or biochemical functions of a naturally
occurring molecule.
Likewise "immunologically active" or "immunological activity" refers t~ the
capability of
the natural, recombinant or synthetic polypeptide to induce a specific immune
response in
appropriate animals or cells and to bind with specific antibodies.
The term "activated cells" as used in this application are those cells which
are
engaged in extracellular or intracellular membrane trafficking, including the
export of
secretory or enzymatic molecules as part of a normal or disease process.
The terms "complementary" or "complementarity" refer to the natural binding of
polynucleotides by base pairing. For example, the sequence 5'-AGT-3' binds to
the
complementary sequence 3'-TCA-5'. Complementarity between two single-stranded
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8
molecules may be "partial" such that only certain portions) of the nucleic
acids bind or it
may be "complete" such that total complementarity exists between the single
stranded
molecules. The degree of complementarity between the nucleic acid strands has
significant
effects on the efficiency and strength of the hybridization between the
nucleic acid strands.
The term "embryonic stem cells (ES)" refers to a cell that can give rise to
many
differentiated cell types in an embryo or an adult, including the germ cells.
The term "germ
line stem cells (GSCs)" refers to stem cells derived from primordial stem
cells that provide a
steady and continuous source of germ cells for the production of gametes. The
term
"primordial germ cells (PGCs)" refers to a small population of cells set aside
from other cell
lineages particularly from the yolk sac, mesenteries, or gonadal ridges during
embryogenesis
that have the potential to differentiate into germ cells and other cells. PGCs
are the source
from which GSCs and ES cells are derived. The PGCs, the GSCs and the ES cells
are
capable of self renewal. Thus these cells not only populate the germ line and
give rise to a
plurality of terminally differentiated cells that comprise the adult
specialized organs, but are
able to regenerate themselves.
The term "expression modulating fragment," EMF, means a series of nucleotides
which modulates the expression ~f an operably linked ~RF or another EMF.
As used herein, a sequence is said to "modulate the expression of an operably
linked
sequence" when the expression of the sequence is altered by the presence of
the EMF.
EMFs include, but are not limited to, promoters, and promoter modulating
sequences
(inducible elements). ~ne class of EMFs are nucleic acid fragments which
induce the
expression of an operably linked ~RF in response to a specific regulatory
factor or
physiological event.
The terms "nucleotide sequence" or "nucleic acid" or "polynucleotide" or
"oligonucleotide" are used interchangeably and refer t~ a heteropolymer of
nucleotides or
the sequence of these nucleotides. These phrases also refer to I~NA or RNA of
genomic or
synthetic origin which may be single-stranded or double-stranded and may
represent the
sense or the antisense strand, to peptide nucleic acid (PNA) or to any DNA-
like or RNA-like
material. In the sequences herein A is adenine, C is cytosine, T is thymine, G
is guanine and
N is A, C, G, or T (CT) or unknown. It is contemplated that where the
polynucleotide is
RNA, the T (thymine) in the sequences provided herein is substituted with U
(uracil).
Generally, nucleic acid segments provided by this invention may be assembled
from
fragments of the genome and short oligonucleotide linkers, or from a series of
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9
oligonucleotides, or from individual nucleotides, to provide a synthetic
nucleic acid which is
capable of being expressed in a recombinant transcriptional unit comprising
regulatory
elements derived from a microbial or viral operon, or a eukaryotic gene.
The teens "oligonucleotide fragment" or a "polynucleotide fragment",
"portion," or
"segment" or "probe" or "primer" are used interchangeably and refer to a
sequence of
nucleotide residues which are at least about 5 nucleotides, more preferably at
least about 7
nucleotides, more preferably at least about 9 nucleotides, more preferably at
least about 11
nucleotides and most preferably at least about 17 nucleotides. The fragment is
preferably
less than about 500 nucleotides, preferably less than about 200 nucleotides,
more preferably
less than about 100 nucleotides, more preferably less than about 50
nucleotides and most
preferably less than 30 nucleotides. Preferably the probe is from about 6
nucleotides to
about 200 nucleotides, preferably from about 15 to about 50 nucleotides, more
preferably
from about 17 to 30 nucleotides and most preferably from about 20 to 25
nucleotides.
Preferably the fragments can be used in polymerase chain reaction (PCR),
various
hybridisation procedures or microarray procedures to identify or amplify
identical or related
parts of mRNA or DNA molecules. A fragment or segment may uniquely identify
each
polynucleotide sequence of the present invention. Preferably the fragment
comprises a
sequence substantially similar to any one of SEQ ID NO: 1-684, or 1369-1966.
Probes may, for example, be used to determine whether specific mRNA molecules
are present in a cell or tissue or to isolate similar nucleic acid sequences
from chromosomal
DNA as described by -SfJalsh et alo (~alsh~ P.S. et al., 1992, PCR Methods
Appl 1:241-250).
They may be labeled by nick translation, I~lenow fill-in reaction, PCR, or
other methods
well knoWll lIl the art. Probes of the present invention, their preparation
and/or labeling are
elaborated in Sambrook, J. et al., 1989, Molecular Cloning: A Laboratory
Manual, Cold
Spring Harbor Laboratory, NY; or Ausubel, F.M. et al., 1989, Current Protocols
in
Molecular Biology, John Wiley & Sons, New York NY, both of which are
incorporated
herein by reference in their entirety.
The nucleic acid sequences of the present invention also include the sequence
information from the nucleic acid sequences of SEQ ID NO: 1-684, or 1369-1966.
The
sequence information can be a segment of any one of SEQ ID NO: 1-684, or 1369-
1966 that
uniquely identifies or represents the sequence information of that sequence of
SEQ ID NO:
1-684, or 1369-1966, or those segments identified in Tables 3A, 3B, 5, 7, or
8. One such
segment can be a twenty-mer nucleic acid sequence because the probability that
a twenty-
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mer is fully matched in the human genome is 1 in 300. In the human genome,
there are three
billion base pairs in one set of chromosomes. Because 42° possible
twenty-mers exist, there
are 300 times more twenty-mers than there are base pairs in a set of human
chromosomes.
Using the same analysis, the probability for a seventeen-mer to be fully
matched in the
5 human genome is approximately 1 in 5. When these segments are used in arrays
for
expression studies, fifteen-mer segments can be used. The probability that the
fifteen-mer is
fully matched in the expressed sequences is also approximately one in five
because
expressed sequences comprise less than approximately 5% of the entire genome
sequence.
Similarly, when using sequence information for detecting a single mismatch, a
segment
10 can be a twenty-five mer. The probability that the twenty-five mer would
appear in a human
genome with a single mismatch is calculated by multiplying the probability for
a full match
(1-4z5) times the increased probability for mismatch at each nucleotide
position (3 x 25). 'The
probability that an eighteen mer with a single mismatch can be detected in an
array for
expression studies is approximately one in five. The probability that a twenty-
mer with a single
mismatch can be detected in a human genome is approximately one in five.
The term "open reading frame," ~12F, means a series of nucleotide triplets
coding for
amino acids without any termination codons and is a sequence translatable into
protein.
The terms "operably linked" or "operably associated" refer to functionally
related
nucleic acid sequences. For example, a promoter is operably associated or
operably linked
with a coding sequence if the promoter controls the transcription of the
coding sequence.
While operably linked nucleic acid sequences can be contiguous and in the same
reading
frame, certain genetic elements e.g. repressor genes are not contiguously
linked to the coding
sequence but still control transcription/translation of the coding sequence.
The term "pluripotent" refers to the capability of a cell to differentiate
into a number
of differentiated cell types that are present in an adult organism. A
pluripotent cell is
restricted in its differentiation capability in comparison to a totipotent
cell.
The terms "polypeptide" or "peptide" or "amino acid sequence" refer to an
oligopeptide, peptide, polypeptide or protein sequence or fragment thereof and
to naturally
occurring or synthetic molecules. A polypeptide "fragment," "portion," or
"segment" is a
stretch of amino acid residues of at least about 5 amino acids, preferably at
least about 7
amino acids, more preferably at least about 9 amino acids and most preferably
at least about
17 or more amino acids. The peptide preferably is not greater than about 200
amino acids,
more preferably less than 150 amino acids and most preferably less than 100
amino acids.
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11
Preferably the peptide is from about 5 to about 200 amino acids. To be active,
any
polypeptide must have sufficient length to display biological and/or
immunological activity.
The term "naturally occurring polypeptide" refers to polypeptides produced by
cells
that have not been genetically engineered and specifically contemplates
various polypeptides
arising from post-translational modifications of the polypeptide including,
but not limited to,
acetylation, carboxylation, glycosylation, phosphorylation, lipidation and
acylation.
The term "translated protein coding portion" means a sequence which encodes
for the
full-length protein which may include any leader sequence or any processing
sequence.
The term "mature protein coding sequence" means a sequence which encodes a
peptide or protein without a signal or leader sequence. The "mature protein
portion" means
that portion of the protein which does not include a signal or leader
sequence. The peptide
may have been produced by processing in the cell which removes any
leader/signal
sequence. The mature protein portion may or may not include the initial
methionine residue.
The methionine residue may be removed from the protein during processing in
the cell. The
peptide may be produced synthetically or the protein may have been produced
using a
polynucleotide only encoding for the mature protein coding sequence.
The term "derivative" refers to polypeptides chemically modified by such
techniques
as ubiquitination, labeling (e.g., with radionuclides or various enzymes),
covalent polymer
attachment such as pegylation (derivatization with polyethylene glycol) and
insertion or
substitution by chemical synthesis of amino acids such as ornithine, which do
not normally
occur in human proteins.
The terns "variant"(or "analog") refers to any polypeptide differing from
naturally
occurring polypeptides by amino acid insertions, deletions, and substitutions,
created using,
a g~., recombinant DNA techniques. Guidance in deterniining which amino acid
residues
may be replaced, added or deleted without abolishing activities of interest,
may be found by
comparing the sequence of the particular polypeptide with that of homologous
peptides and
minimizing the number of amino acid sequence changes made in regions of high
homology
(conserved regions) or by replacing amino acids with consensus sequence.
Alternatively, recombinant variants encoding these same or similar
polypeptides may
be synthesized or selected by making use of the "redundancy" in the genetic
code. Various
codon substitutions, such as the silent changes which produce various
restriction sites, may
be introduced to optimize cloning into a plasmid or viral vector or expression
in a particular
prokaryotic or eukaryotic system. Mutations in the polynucleotide sequence may
be
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12
reflected in the polypeptide or domains of other peptides added to the
polypeptide to modify
the properties of any part of the polypeptide, to change characteristics such
as ligand-binding
affinities, interchain affinities, or degradation/turnover rate.
Preferably, amino acid "substitutions" are the result of replacing one amino
acid with
another amino acid having similar structural and/or chemical properties, i.e.,
conservative
amino acid replacements. "Conservative" amino acid substitutions may be made
on the
basis of similarity in polarity, charge, solubility, hydrophobicity,
hydrophilicity, and/or the
amphipathic nature of the residues involved. For example, nonpolar
(hydrophobic) amino
acids include alanine, leucine, isoleucine, valine, proline, phenylalanine,
tryptophan, and
methionine; polar neutral amino acids include glycine, serine, threonine,
cysteine, tyrosine,
asparagine, and glutamine; positively charged (basic) amino acids include
arginine, lysine,
and histidine; and negatively charged (acidic) amino acids include aspartic
acid and glutamic
acid. "Insertions" or "deletions" are preferably in the range of about 1 to 20
amino acids,
more preferably 1 to 10 amino acids. The variation allowed may be
experimentally
determined by systematically making insertions, deletions, or substitutions of
amino acids in
a polypeptide molecule using recombinant DI~~ techniques and assaying the
resulting
recombinant variants for activity.
Alternatively, where alteration of function is desired, insertions, deletions
or
non-conservative alterations can be engineered to produce altered
polypeptides. Such
alterations can, for example, alter one or more of the biological functions or
biochemical
characteristics of the polypeptides of the invention. For ea~ample, such
alterations may
change polypeptide characteristics such as ligand-binding affinities,
interchain affinities, or
degradation/turnover rate. Further, such alterations can be selected so as to
generate
polypeptides that are better suited for expression, scale up and the like in
the host cells
chosen for expression. For example, cysteine residues can be deleted or
substituted with
another amino acid residue in order to eliminate disulfide bridges.
The terms "purified" or "substantially purified" as used herein denotes that
the
indicated nucleic acid or polypeptide is present in the substantial absence of
other biological
macromolecules, e.g., polynucleotides, proteins, and the like. In one
embodiment, the
polynucleotide or polypeptide is purified such that it constitutes at least
95% by weight,
more preferably at least 99% by weight, of the indicated biological
macromolecules present
(but water, buffers, and other small molecules, especially molecules having a
molecular
weight of less than 1000 daltons, can be present).
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13
The term "isolated" as used herein refers to a nucleic acid or polypeptide
separated
from at least one other component (e.g., nucleic acid or polypeptide) present
with the nucleic
acid or polypeptide in its natural source. In one embodiment, the nucleic acid
or polypeptide
is found in the presence of (if anything) only a solvent, buffer, ion, or
other component
normally present in a solution of the same. The terms "isolated" and
"purified" do not
encompass nucleic acids or polypeptides present in their natural source.
The term "recombinant," when used herein to refer to a polypeptide or protein,
means
that a polypeptide or protein is derived from recombinant (e.g., microbial,
insect, or
mammalian) expression systems. "Microbial" refers to recombinant polypeptides
or proteins
made in bacterial or fungal (e.g., yeast) expression systems. As a product,
"recombinant
microbial" defines a polypeptide or protein essentially free of native
endogenous substances
and unaccompanied by associated native glycosylation. Polypeptides or proteins
expressed
in most bacterial cultures, e.g., E. coli, will be free of glycosylation
modifications;
polypeptides or proteins expressed in yeast will have a glycosylation pattern
in general
different from those expressed in mammalian cells.
The term "recombinant expression vehicle or vector" refers to a plasmid or
phage or
virus or vector, fox expressing a polypeptide from a DNA (RNA) sequence. An
expression
vehicle can comprise a transcriptional unit comprising an assembly of (1) a
genetic element
or elements having a regulatory role in gene expression, for example,
promoters or
enhancers, (2) a structural or coding sequence which is transcribed into mRNA
and
translated into protein, and (3) appropriate transcription initiation and
termination sequences.
Structural units intended for use in yeast or eukaryotic expression systems
preferably include
a leader sequence enabling extracellular secretion of translated protein by a
host cell.
Alternatively, where recombinant protein is expressed without a leader or
transport
sequence, it may include an amino terminal methionine residue. This residue
may or may
not be subsequently cleaved from the expressed recombinant protein to provide
a anal
product.
The term "recombinant expression system" means host cells which have stably
integrated a recombinant transcriptional unit into chromosomal DNA or carry
the
recombinant transcriptional unit extrachromosomally. Recombinant expression
systems as
defined herein will express heterologous polypeptides or proteins upon
induction of the
regulatory elements linked to the DNA segment or synthetic gene to be
expressed. This term
also means host cells which have stably integrated a recombinant genetic
element or
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14
elements having a regulatory role in gene expression, for example, promoters
or enhancers.
Recombinant expression systems as defined herein will express polypeptides or
proteins
endogenous to the cell upon induction of the regulatory elements linked to the
endogenous
DNA segment or gene to be expressed. The cells can be prokaryotic or
eukaryotic.
The term "secreted" includes a protein that is transported across or through a
membrane, including transport as a result of signal sequences in its amino
acid sequence
when it is expressed in a suitable host cell. "Secreted" proteins include
without limitation
proteins secreted wholly (e.g., soluble proteins) or partially (e.g.,
receptors) from the cell in
which they are expressed. "Secreted" proteins also include without limitation
proteins that
are transported across the membrane of the endoplasmic reticulum. "Secreted"
proteins are
also intended to include proteins containing non-typical signal sequences
(e.g. Interleukin-1
Beta, see I~rasney, P.A. and Young, P.R. (1992) Cytokine 4(2): 134 -143) and
factors
released from damaged cells (e.g. Interleukin-1 Receptor Antagonist, see
Arend, W.P. et. al.
(1990 Annu. Rev. Immunol. 16:27-55)
Where desired, an expression vector may be designed to contain a "signal or
leader
sequence" which will direct the polypeptide through the membrane of a cell.
Such a
sequence may be naturally present on the polypeptides of the present invention
or provided
from heterologous protein sources by recombinant DNA techniques.
The term "stringent" is used to refer to conditions that are commonly
understood in
the art as stringent. Stringent conditions can include highly stringent
conditions (i.e.,
hybridization to alter-bound DNA in 0.5 l~Jl NaIiP~4.~ 7% sodium dodecyl
sulfate (SDS), 1
mI~ EDTA at 65°C, and washing in 0.1~ SSC/0.1% SDS at 6S°C), and
moderately stringent
conditions (i.e., washing in 0.2X SSC/0.1% SDS at 42°C). ~ther
exemplary hybridization
conditions are described herein in the examples.
In instances of hybridization of deoxyoligonucleotides, additional exemplary
stringent hybridization conditions include washing in 6~ SSC/0.05% sodium
pyrophosphate
at 37°C (for 14-base oligonucleotides), 4~°C (for 17-base
oligonucleotides), 55°C (for 20-
base oligonucleotides), and 60°C (for 23-base oligonucleotides).
As used herein, "substantially equivalent" or "substantially similar" can
refer both to
nucleotide and amino acid sequences, for example a mutant sequence, that
varies from a
reference sequence by one or more substitutions, deletions, or additions, the
net effect of
which does not result in an adverse functional dissimilarity between the
reference and
subject sequences. Typically, such a substantially equivalent sequence varies
from one of
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those listed herein by no more than about 35% (i.e., the number of individual
residue
substitutions, additions, and/or deletions in a substantially equivalent
sequence, as compared
to the corresponding reference sequence, divided by the total number of
residues in the
substantially equivalent sequence is about 0.35 or less). Such a sequence is
said to have
5 65% sequence identity to the listed sequence. In one embodiment, a
substantially
equivalent, e.g., mutant, sequence of the invention varies from a listed
sequence by no more
than 30% (70% sequence identity); in a variation of this embodiment, by no
more than 25%
(75% sequence identity); and in a further variation of this embodiment, by no
more than
20% (80% sequence identity) and in a further variation of this embodiment, by
no more than
10 10% (90% sequence identity) and in a further variation of this embodiment,
by no more that
5% (95% sequence identity). Substantially equivalent, e.g., mutant, amino acid
sequences
according to the invention preferably have at least 80% sequence identity with
a listed amino
acid sequence, more preferably at least 85% sequence identity, more preferably
at least 90°/~
sequence identity, more preferably at least 95% sequence identity, more
preferably at least
15 98% sequence identity, and most preferably at least 99°/~ sequence
identity. Substantially
equivalent nucleotide sequence of the invention can have lower percent
sequence identities,
taking into account, for example, the redundancy or degeneracy of the genetic
code.
Preferably, the nucleotide sequence has at least about 65% identity, more
preferably at least
about 75% identity, more preferably at least about 80% sequence identity, more
preferably at
least 85% sequence identity, more preferably at least 90% sequence identity,
more preferably
at least about 95% sequence identity9 more preferably at least 98% sequence
identity, and
most preferably at least 99% sequence identity. For the purposes of the
present invention,
sequences having substantially equivalent biological activity and
substantially equivalent
expression characteristics are considered substantially equivalent. For the
purposes of
determining equivalence, truncation of the mature sequence (e.g., via a
mutation which
creates a new stop codon) should be disregarded. Sequence identity may be
determined,
e.g., using the Jotun Hein method (Hero, J. (1990) Methods Enzymol. 183:626-
645).
Identity between sequences can also be determined by other methods known in
the art, e.g.
by varying hybridization conditions.
The term "totipotent" refers to the capability of a cell to differentiate into
all of the
cell types of an adult organism.
The term "transformation" means introducing DNA into a suitable host cell so
that
the DNA is replicable, either as an extrachromosomal element, or by
chromosomal
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16
integration. The term "transfection" refers to the taking up of an expression
vector by a
suitable host cell, whether or not any coding sequences are in fact expressed.
The term
"infection" refers to the introduction of nucleic acids into a suitable host
cell by use of a
virus or viral vector.
As used herein, an "uptake modulating fragment," UMF, means a series of
nucleotides which mediate the uptake of a linked DNA fragment into a cell.
UMFs can be
readily identified using known UMFs as a target sequence or target motif with
the
computer-based systems described below. The presence and activity of a UMF can
be
confirmed by attaching the suspected UMF to a marker sequence. The resulting
nucleic acid
molecule is then incubated with an appropriate host under appropriate
conditions and the
uptake of the marker sequence is determined. As described above, a UMF will
increase the
frequency of uptake of a linked marker sequence.
Each of the above terms is meant to encompass all that is described for each,
unless
the context dictates otherwise.
4.2 T'~iJCI~EIC ALIDS OF TIC IN~EI~'I"I~1~
Nucleotide sequences of the invention are set forth in the Sequence Listing.
The isolated polynucleotides of the invention include a polynucleotide
comprising
the nucleotide sequences of SEQ ID NO: 1-684, or 1369-1966; a polynucleotide
encoding
any one of the peptide sequences of SEQ ID NO: 1-684, or 1369-1966; and a
polynucleotide
comprising the nucleotide sequence encoding the mature protein coding sequence
of the
polynucleotides of any one of SEQ ID NO: 1-684, or 1369-1966. The
polynucleotides of the
present invention also include, but are not limited to, a polynucleotide that
hybridises under
stringent conditions to (a) the complement of any of the nucleotides sequences
of SEQ ID
NO: 1-684, or 1369-1966; (b) nucleotide sequences encoding any one of the
amino acid
sequences set forth in the Sequence Listing, or Table 7; (c) a polynucleotide
which is an
allelic variant of any polynucleotide recited above; (d) a polynucleotide
which encodes a
species homologue of any of the proteins recited above; or (e) a
polynucleotide that encodes
a polypeptide comprising a specific domain or truncation of the polypeptides
of SEQ ID NO:
685-1368, or 1967-2564 (for example, as set forth in Tables 3A, 3B, 5, 7, or
8). Domains of
interest may depend on the nature of the encoded polypeptide; e.g., domains in
receptor-like
polypeptides include ligand-binding, extracellular, transmembrane, or
cytoplasmic domains,
or combinations thereof; domains in immunoglobulin-like proteins include the
variable
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17
immunoglobulin-like domains; domains in enzyme-like polypeptides include
catalytic and
substrate binding domains; and domains in ligand polypeptides include receptor-
binding
domains.
The polynucleotides of the invention include naturally occurring or wholly or
partially synthetic DNA, e.g., cDNA and genomic DNA, and RNA, e.g., mRNA. The
polynucleotides may include entire coding region of the cDNA or may represent
a portion of
the coding region of the cDNA.
The present invention also provides genes corresponding to the cDNA sequences
disclosed herein. The corresponding genes can be isolated in accordance with
known methods
using the sequence information disclosed herein. Such methods include the
preparation of
probes or primers from the disclosed sequence information for identification
and/or
amplification of genes in appropriate genomic libraries or other sources of
genomic materials.
Further 5' and 3' sequence can be obtained using methods known in the art. For
example, full
length cDNA or genomic DNA that corresponds to any of the polynucleotides of
SEQ ~ NO:
1-684, or 1369-1966 can be obtained by screening appropriate cDNA or genomic
DNA
libraries under suitable hybridization conditions using any of the
polynucleotides of SEQ ff~
NO: 1-684, or 1369-1966 or a portion thereof as a probe. Alternatively, the
polynucleotides of
SEQ ~ NO: 1-684, or 1369-1966 may be used as the basis for suitable primers)
that allow
identification and/or amplification of genes in appropriate genomic DNA or
cDNA libraries.
The nucleic acid sequences of the invention can be assembled from ESTs and
sequences
(including cDNA and genomic sequences) obtained from one er more public
databases, such as
dbEST, gbpri, and LTniGene. The EST sequences can provide identifying sequence
information, representative fragment ~r segment information, or novel segment
information for
the full-length gene.
The polynucleotides of the invention also provide polynucleotides including
nucleotide sequences that are substantially equivalent to the polynucleotides
recited above.
Polynucleotides according to the invention can have, e.~., at least about 65%,
at least about
70%, at least about 75%, at least about 80%, 81%, 82%, 83%, 84°/~, more
typically at least
about 85%, 86%, 87%, 88%, 89%, more typically at least about 90%, 91%, 92%,
93%, 94%,
and even more typically at least about 95%, 96%, 97%, 98%, 99% sequence
identity to a
polynucleotide recited above.
Included within the scope of the nucleic acid sequences of the invention are
nucleic
acid sequence fragments that hybridize under stringent conditions to any of
the nucleotide
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18
sequences of SEQ ID NO: 1-684, or 1369-1966, or complements thereof, which
fragment is
greater than about 5 nucleotides, preferably 7 nucleotides, more preferably
greater than 9
nucleotides and most preferably greater than 17 nucleotides. Fragments of,
e.g. 15, 17, or 20
nucleotides or more that are selective for (i.e. specifically hybridize to)
any one of the
polynucleotides of the invention are contemplated. Probes capable of
specifically
hybridizing to a polynucleotide can differentiate polynucleotide sequences of
the invention
from other polynucleotide sequences in the same family of genes or can
differentiate human
genes from genes of other species, and are preferably based on unique
nucleotide sequences.
The sequences falling within the scope of the present invention are not
limited to these
specific sequences, but also include allelic and species variations thereof.
Allelic and species
variations can be routinely determined by comparing the sequence provided in
SEQ ID NO: 1-
684, or 1369-1966, a representative fragment thereof, or a nucleotide sequence
at least 90%
identical, preferably 95°!° identical, to SEQ ID NO: 1-684, or
1369-1966 with a sequence from
another isolate of the same species. Furthermore, to accommodate colon
variability, the
invention includes nucleic acid molecules coding for the same amino acid
sequences as do the
specific OIZFs disclosed herein. In other words, in the coding region of an
OIZF, substitution of
one colon for another colon that encodes the same amin~ acid is expressly
contemplated.
The nearest neighbor or homology results for the nucleic acids ~f the present
invention,
including SEQ ID NO: 1-684, or 1369-1966 can be obtained by searching a
database using an
algorithm or a program. Preferably, a BLAST (Basic Local Alignment Search
Tool) program is
used t~ search for local sequence alignments (Altshul, S.F. J I~IoI. Evol. 36
290-300 (1993) and
Altschul S.F. et al. J. I~IoI. Biol. 21:403-410 (1990)). Alternatively a PASTA
versi~n 3 search
against Genpept, using FAST' algorithm may be performed.
Species homologs (or orthologs) of the disclosed polynucleotides and proteins
are
also provided by the present invention. Species homologs may be isolated and
identified by
making suitable probes or primers from the sequences provided herein and
screening a
suitable nucleic acid source from the desired species.
The invention also encompasses allelic variants of the disclosed
polynucleotides or
proteins; that is, naturally-occurring alternative forms of the isolated
polynucleotide which
also encode proteins which are identical, homologous or related to that
encoded by the
polynucleotides.
The nucleic acid sequences of the invention are further directed to sequences
which
encode variants of the described nucleic acids. These amino acid sequence
variants may be
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19
prepared by methods known in the art by introducing appropriate nucleotide
changes into a
native or variant polynucleotide. There are two variables in the construction
of amino acid
sequence variants: the location of the mutation and the nature of the
mutation. Nucleic
acids encoding the amino acid sequence variants are preferably constructed by
mutating the
polynucleotide to encode an amino acid sequence that does not occur in nature.
These
nucleic acid alterations can be made at sites that differ in the nucleic acids
from different
species (variable positions) or in highly conserved regions (constant
regions). Sites at such
locations will typically be modified in series, e.g., by substituting first
with conservative
choices (e.g., hydrophobic amino acid to a different hydrophobic amino acid)
and then with
more distant choices (e.g., hydrophobic amino acid to a charged amino acid),
and then
deletions or insertions may be made at the target site. Amino acid sequence
deletions
generally range from about 1 to 30 residues, preferably about 1 to 10
residues, and are
typically contiguous. Amino acid insertions include amino- and/or carboxyl-
terminal
fusions ranging in length from one t~ one hundred or more residues, as well as
intrasequence
insertions of single or multiple amino acid residues. Intrasequence insertions
may range
generally from about 1 to 10 amino residues, preferably from 1 to 5 residues.
Examples of
terminal insertions include the heterologous signal sequences necessary for
secretion or for
intracellular targeting in different host cells and sequences such as FLAG or
poly-histidine
sequences useful for purifying the expressed protein.
In a preferred method, polynucleotides encoding the novel amino acid sequences
are
changed via site-directed muta.genesis. This method uses oligonucle~tide
sequences to alter
a polynucleotide to encode the desired amino acid variant, as well as
sufficient adjacent
nucle~tides on both sides of the changed amino acid to form a stable duplex on
either side of
the site of being changed. In general, the techniques of site-directed
mutagenesis are well
known to those of skill in the art and this technique is exemplified by
publications such as,
Edelman et al., I~NA 2:183 (1983). A versatile and efficient method for
producing
site-specific changes in a polynucleotide sequence was published by Zoller and
Smith,
Nucleic Acids Res. 10:6487-6500 (1982). PCR may also be used to create amino
acid
sequence variants of the novel nucleic acids. When small amounts of template
DNA are
used as starting material, primers) that differs slightly in sequence from the
corresponding
region in the template DNA can generate the desired amino acid variant. PCR
amplification
results in a population of product DNA fragments that differ from the
polynucleotide
template encoding the polypeptide at the position specified by the primer. The
product DNA
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fragments replace the corresponding region in the plasmid and this gives a
polynucleotide
encoding the desired amino acid variant.
A further technique for generating amino acid variants is the cassette
mutagenesis
technique described in Wells et al., Gene 34:315 (1985); and other mutagenesis
techniques
5 well known in the art, such as, for example, the techniques in Sambrook et
al., supra, and
Currefat Protocols in Molecular Biology, Ausubel et al. Due to the inherent
degeneracy of
the genetic code, other DNA sequences which encode substantially the same or a
functionally equivalent amino acid sequence may be used in the practice of the
invention for
the cloning and expression of these novel nucleic acids. Such DNA sequences
include those
10 which are capable of hybridizing to the appropriate novel nucleic acid
sequence under
stringent conditions.
Polynucleotides encoding preferred polypeptide truncations of the invention
could be
used to generate polynucleotides encoding chimeric or fusion proteins
comprising one or
more domains of the invention and heterologous protein sequences.
15 The polynucleotides of the invention additionally include the complement of
any of
the polynucleotides recited above. The polynucleotide can be DNA (genomic,
cDNA,
amplified, or synthetic) or RNA. Methods and algorithms for obtaining such
polynucleotides are well known to those of skill in the art and can include,
for example,
methods for determining hybridization conditions that can routinely isolate
polynucleotides
20 of the desired sequence identities.
In accordance vJith the invention, polynucleotide sequences comprising the
mature
protein coding sequences corresponding to any one of SEQ ID N~: 1-684, or 1369-
1966, or
functional equivalents thereof, may be used to generate recombinant DNA
molecules that
direct the expression of that nucleic acid, or a functional equivalent
thereof, in appropriate
host cells. Also included are the cDNA inserts of any of the clones identified
herein.
A polynucleotide according to the invention can be joined to any of a variety
of other
nucleotide sequences by well-established recombinant DNA techniques (see
Sambrook J et
al. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor
Laboratory, NY).
Useful nucleotide sequences for joining to polynucleotides include an
assortment of vectors,
e.g., plasmids, cosmids, lambda phage derivatives, phagemids, and the like,
that are well
known in the art. Accordingly, the invention also provides a vector including
a
polynucleotide of the invention and a host cell containing the polynucleotide.
In general, the
vector contains an origin of replication functional in at least one organism,
convenient
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21
restriction endonuclease sites, and a selectable marker for the host cell.
Vectors according to
the invention include expression vectors, replication vectors, probe
generation vectors, and
sequencing vectors. A host cell according to the invention can be a
prokaryotic or
eukaryotic cell and can be a unicellular organism or part of a multicellular
organism.
The present invention further provides recombinant constructs comprising a
nucleic
acid having any of the nucleotide sequences of SEQ ID NO: 1-684, or 1369-1966
or a
fragment thereof or any other polynucleotides of the invention. In one
embodiment, the
recombinant constructs of the present invention comprise a vector, such as a
plasmid or viral
vector, into which a nucleic acid having any of the nucleotide sequences of
SEQ ID NO: 1-
684, or 1369-1966 or a fragment thereof is inserted, in a forward or reverse
orientation. In
the case of a vector comprising one of the ORFs of the present invention, the
vector may
further comprise regulatory sequences, including for example, a promoter,
operably linked to
the ORF. Large numbers of suitable vectors and promoters are known to those of
skill in the
art and are commercially available for generating the recombinant constructs
of the present
invention. The following vectors are provided by way of example: Bacterial:
pBs,
phagescript, PsiX174, pFluescript SIB, pBs IBS, pNI38a, pNHl6a, pNI318a,
pNII46a
(Stratagene), pTrc99A, p 23-3, pI~233-3, pDR540, pRITS (Pharmacia);
Eukaryotic:
pWLneo, pSV2cat, pOG44, PXTI, pSG (Stratagene) pSVI~3, pBPV, pMSG, pSVL
(Pharmacia).
The isolated polynucleotide of the invention may be operably linked to an
expression
c~ntr~1 sequence such as the pMT2 or pED expression vectors disclosed in
I~aufman et al.,
Naceleic Acids yes. 19, 4485-4490 (1991), in order to produce the protein
recombinantly.
Many suitable expression control sequences are kn~wn in the art. General
methods of
expressing recombinant proteins are also known and are exemplified in R.
I~aufman,
Methods in EaZZymol~gy 185, 537-566 (1990). As defined herein "operably
linked" means
that the isolated polynucleotide of the invention and an expression control
sequence are
situated within a vector or cell in such a way that the protein is expressed
by a host cell
which has been transformed (transfected) with the ligated
polynucleotide/expression control
sequence.
Promoter regions can be selected from any desired gene using CAT
(chloramphenicol transferase) vectors or other vectors with selectable
markers. Two
appropriate vectors are pKI~232-8 and pCM7. Particular named bacterial
promoters include
lacI, lac2, T3, T7, gpt, lambda PR, and trc. Eukaryotic promoters include CMV
immediate
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early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and
mouse
metallothionein-I. Selection of the appropriate vector and promoter is well
within the level
of ordinary skill in the art. Generally, recombinant expression vectors will
include origins of
replication and selectable markers permitting transformation of the host cell,
e.g., the
ampicillin resistance gene of E. coli and S. ce~evisiae TRP 1 gene, and a
promoter derived
from a highly expressed gene to direct transcription of a downstream
structural sequence.
Such promoters can be derived from operons encoding glycolytic enzymes such as
3-
phosphoglycerate kinase (PGK), a-factor, acid phosphatase, or heat shock
proteins, among
others. The heterologous structural sequence is assembled in appropriate phase
with
translation initiation and termination sequences, and preferably, a leader
sequence capable of
directing secretion of translated protein into the periplasmic space or
extracellular medium.
Optionally, the heterologous sequence can encode a fusion protein including an
amino
terminal identification peptide imparting desired characteristics, e.g.,
stabilization or
simplified purification of expressed recombinant product. Useful expression
vectors for
bacterial use are c~nstructed by inserting a structural DNA sequence encoding
a desired
protein t~gether with suitable translation initiation and termination signals
in operable
reading phase with a functional promoter. 'The vector will comprise one ~r
more phenotypic
selectable markers and an origin of replication to ensure maintenance of the
vector and to, if
desirable, provide amplification within the host. Suitable prokaryotic hosts
for
transformation include E. coli, Bacillus subtilis, Salmofaella t~phir~aurium
and various species
within the genera Pseac~~araacyaas, Sta°e~at~anyces, and
Sta~alayl~c~ccus, although others may
also be employed as a matter of choice.
As a representative but n~n-limiting example, useful expression vectors for
bacterial
use can comprise a selectable marker and bacterial origin of replication
derived from
commercially available plasmids comprising genetic elements of the well known
cloning
vector pBR32,2 (ATCC 37017). Such commercial vectors include, for example,
pKK223-3
(Pharmacia Fine Chemicals, Uppsala, Sweden) and GEM 1 (Promega Biotech,
Madison, WI,
USA). These pBR322 "backbone" sections are combined with an appropriate
promoter and
the structural sequence to be expressed. Following transformation of a
suitable host strain
and growth of the host strain to an appropriate cell density, the selected
promoter is induced
or derepressed by appropriate means (e.g., temperature shift or chemical
induction) and cells
are cultured for an additional period. Cells are typically harvested by
centrifugation,
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23
disrupted by physical or chemical means, and the resulting crude extract
retained for further
purification.
Polynucleotides of the invention can also be used to induce immune responses.
For
example, as described in Fan et al., Nat. Biotech 17, 870-872 (1999),
incorporated herein by
reference, nucleic acid sequences encoding a polypeptide may be used to
generate antibodies
against the encoded polypeptide following topical administration of naked
plasmid DNA or
following injection, and preferably infra-muscular injection of the DNA. The
nucleic acid
sequences are preferably inserted in a recombinant expression vector and may
be in the form
of naked DNA.
4.3 ANTISENSE
Another aspect of the invention pertains to isolated antisense nucleic acid
molecules
that are hybridizable to or complementary to the nucleic acid molecule
comprising the
nucleotide sequence of SEQ ID NO: 1-684, or 1369-1966, or fragments, analogs
or
derivatives thereof. An "antisense" nucleic acid comprises a nucleotide
sequence that is
complementary to a "sense" nucleic acid encoding a protein, e.g.,
complementary to the
coding strand of a double-stranded cDNA molecule or complementary to an mRNA
sequence. In specific aspects, antisense nucleic acid molecules are provided
that c~mprise a
sequence complementary to at least about 10, 25, 50, 100, 250 or 500
nucleotides or an
entire coding strand, or to only a portion thereof. Nucleic acid molecules
encoding
fragments, homologs, derivatives and analogs of a protein of any of SEQ ID NO:
1-684, or
1369-1966 or antisense nucleic acids complementary to a nucleic acid sequence
of SEQ ID
NO: 1-684, or 1369-1966 are additionally provided.
In one embodiment, an antisense nucleic acid molecule is antisense to a
"coding
region" of the coding strand of a nucleotide sequence of the invention. The
ternz "coding
region" refers to the region of the nucleotide sequence comprising colons
which are
translated into amino acid residues. In another embodiment, the antisense
nucleic acid
molecule is antisense to a "noncoding region" of the coding strand of a
nucleotide sequence
of the invention. The term "noncoding region" refers to 5' and 3' sequences
that flank the
coding region that are not translated into amino acids (i.e., also referred to
as 5' and 3'
untranslated regions).
Given the coding strand sequences encoding a nucleic acid disclosed herein
(e.g.,
SEQ ID NO: 1-684, or 1369-1966, antisense nucleic acids of the invention can
be designed
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24
according to the rules of Watson and Crick or Hoogsteen base pairing. The
antisense nucleic
acid molecule can be complementary to the entire coding region of an mRNA, but
more
preferably is an oligonucleotide that is antisense to only a portion of the
coding or noncoding
region of an mRNA. For example, the antisense oligonucleotide can be
complementary to
the region surrounding the translation start site of an mRNA. An antisense
oligonucleotide
can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides
in length. An
antisense nucleic acid of the invention can be constructed using chemical
synthesis or
enzymatic ligation reactions using procedures known in the art. For example,
an antisense
nucleic acid (e.g., an antisense oligonucleotide) can be chemically
synthesized using
naturally occurnng nucleotides or variously modified nucleotides designed to
increase the
biological stability of the molecules or to increase the physical stability of
the duplex formed
between the antisense and sense nucleic acids, e.g., phosphorothioate
derivatives and
acridine substituted nucleotides can be used.
Examples of modified nucleotides that can be used to generate the antisense
nucleic
acid include: 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil,
hypoxanthine,
xanthine, 4-acetylcytosine, 5-(carboxyhydroxyhxaethyl) uracil, 5-
carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil,
dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-
methylguanine,
1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-
methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-
methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-
mannosylqueosine,
5'-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-
isopentenyladenine,
uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-
thiocytosine, 5-methyl-
2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic
acid methylester,
uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2-
carboxypropyl) uracil,
(acp3)w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can
be produced
biologically using an expression vector into which a nucleic acid has been
subcloned in an
antisense orientation (i.e., RNA transcribed from the inserted nucleic acid
will be of an
antisense orientation to a target nucleic acid of interest, described further
in the following
subsection).
The antisense nucleic acid molecules of the invention are typically
administered to a
subject or generated ira situ such that they hybridize with or bind to
cellular mRNA and/or
genomic DNA encoding a protein according to the invention to thereby inhibit
expression of
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the protein, e.g., by inhibiting transcription andlor translation. The
hybridization can be by
conventional nucleotide complementarity to form a stable duplex, or, for
example, in the
case of an antisense nucleic acid molecule that binds to DNA duplexes, through
specific
interactions in the major groove of the double helix. An example of a route of
5 administration of antisense nucleic acid molecules of the invention includes
direct injection
at a tissue site. Alternatively, antisense nucleic acid molecules can be
modified to target
selected cells and then administered systemically. For example, for systemic
administration,
antisense molecules can be modified such that they specifically bind to
receptors or antigens
expressed on a selected cell surface, e.g., by linking the antisense nucleic
acid molecules to
10 peptides or antibodies that bind to cell surface receptors or antigens. The
antisense nucleic
acid molecules can also be delivered to cells using the vectors described
herein. To achieve
sufficient intracellular concentrations of antisense molecules, vector
constructs in which the
antisense nucleic acid molecule is placed under the control of a strong pol II
or pol III
promoter are preferred.
15 In yet another embodiment, the antisensc nucleic acid molecule of the
invention is an
ce-anomeric nucleic acid molecule. An ~,-anomeric nucleic acid molecule forms
specific
double-stranded hybrids with complementary RNA in which, contrary to the usual
oc-units,
the strands run parallel to each other (Gaultier et al. (1987) Nucleic Acids
lees 15:
6625-6641). The antisense nucleic acid molecule can also comprise a
20 2'-o-methylribonucleotide (moue et al. (1987) Nucleic Acids Res 15: 6131-
6148) or a
chimeric RNA -DNA analogue (Inoue et al. (1987) ~R"R~'Lett 215: 32?-330).
4.4 I~I~~~S AND PNA 1~IOIETyES
In still another embodiment, an antisense nucleic acid of the invention is a
ribozyme.
25 Ribozymes are catalytic RNA molecules with ribonuclease activity that are
capable of
cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a
complementary region. Thus, ribozymes (e.g., hammerhead ribozymes (described
in
Haselhoff and Gerlach (1988) Nature 334:585-591)) can be used to catalytically
cleave
mRNA transcripts to thereby inhibit translation of an mRNA. A ribozyme having
specificity
for a nucleic acid of the invention can be designed based upon the nucleotide
sequence of a
DNA disclosed herein (i.e., SEQ ID NO: 1-684, or 1369-1966). For example, a
derivative of
Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence
of the
active site is complementary to the nucleotide sequence to be cleaved in a
mRNA. See, e.g.,
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26
Cech et al. U.S. Pat. No. 4,987,071; and Cech et al. U.S. Pat. No. 5,116,742.
Alternatively,
mRNA of the invention can be used to select a catalytic RNA having a specific
ribonuclease
activity from a pool of RNA molecules. See, e.g., Bartel et al., (1993)
Sciezzce
261:1411-1418.
Alternatively, gene expression can be inhibited by targeting nucleotide
sequences
complementary to the regulatory region (e.g., promoter and/or enhancers) to
form triple
helical structures that prevent transcription of the gene in target cells. See
generally, Helens.
(1991) Anticancer Dz-ug Des. 6: 569-84; Helens. et al. (1992) Arz>z. N. Y.
Acad. Sci.
660:27-36; and Maher (1992) Bioassays 14: 807-15.
In various embodiments, the nucleic acids of the invention can be modified at
the
base moiety, sugar moiety or phosphate backbone to improve, e.g., the
stability,
hybridization, or solubility of the molecule. For example, the deoxyribose
phosphate
backbone of the nucleic acids can be modified to generate peptide nucleic
acids (see Hyrup
et al. (1996) Bioorg Med C'laezzz 4: 5-23). As used herein, the terms "peptide
nucleic acids"
or "PNAs" refer to nucleic acid mimics, e.g., DNA mimics, in which the
deoxyribose
phosphate backbone is replaced by a pseudopeptide backbone and only the four
natural
nucleobases are retained. The neutral backbone of PNAs has been shown to allow
for
specific hybridization to DNA and RNA under conditions of low ionic strength.
The
synthesis of PNA oligomers can be performed using standard solid phase peptide
synthesis
protocols as described in Hyrup et al. (1996) above; Perry-O'I~eefe et al.
(1996) PNAS' 93:
14670-67~.
PNAs of the invention can be used in therapeutic and diagnostic applications.
For
example, PNAs can be used as antisense or antigens agents for sequence-
specific modulation
of gene expression by, e.g., inducing transcription or translation arrest or
inhibiting
replication. PNAs of the invention can also be used, e.g., in the analysis of
single base pair
mutations in a gene by, e.g., PNA directed PCR clamping; as artificial
restriction enzymes
when used in combination with other enzymes, e.g., Sl nucleases (Hyrup B.
(1996) above);
or as probes or primers for DNA sequence and hybridization (Hyrup et al.
(1996), above;
Perry-O'Keefe (1996), above).
In another embodiment, PNAs of the invention can be modified, e.g., to enhance
their stability or cellular uptake, by attaching lipophilic or other helper
groups to PNA, by
the formation of PNA-DNA chimeras, or by the use of liposomes or other
techniques of drug
delivery known in the art. For example, PNA-DNA chimeras can be generated that
may
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27
combine the advantageous properties of PNA and DNA. Such chimeras allow DNA
recognition enzymes, e.g., RNase H and DNA polymerases, to interact with the
DNA
portion while the PNA portion would provide high binding affinity and
specificity.
PNA-DNA chimeras can be linked using linkers of appropriate lengths selected
in terms of
base stacking, number of bonds between the nucleobases, and orientation (Hyrup
(1996)
above). The synthesis of PNA-DNA chimeras can be performed as described in
Hyrup
(1996) above and Finn et al. (1996) Nucl Acids Res 24: 3357-63. For example, a
DNA chain
can be synthesized on a solid support using standard phosphoramidite coupling
chemistry,
and modified nucleoside analogs, e.g., 5'-(4-methoxytrityl)amino-5'-deoxy-
thymidine
phosphoramidite, can be used between the PNA and the 5' end of DNA (Mag et al.
(1989)
Nucl Acid Res 17: 5973-88). PNA monomers are then coupled in a stepwise manner
to
produce a chimeric molecule with a 5' PNA segment and a 3' DNA segment (Finn
et al.
(1996) above). Alternatively, chimeric molecules can be synthesized with a 5'
DNA
segment and a 3' PNA segment. See, Petersen et al. (1975) Bioorg Med Claezn
Lett 5:
1119-11124.
In other embodiments, the oligonucleotide may include other appended groups
such
as peptides (e.g., for targeting host cell receptors in viv~), or agents
facilitating transport
across the cell membrane (see, e.g., Letsinger et al., 1989, Proc. Natl. Acad.
~'ci. ZJ:S.A.
86:6553-6556; Lemaitre et al., 1987, Proc. Natl. Acad. Sci. 84:648-652; PCT
Publication
No. W088/09810) or the blood-brain barrier (see, e.g., PCT Publication No.
W089/10134).
In addition, oligonucleotides can be modified with hybridization triggered
cleavage agents
(See, e.g., I~rol et al., 1988, Bi~T'eclzzziques 6:958-976) or intercalating
agents. (See e.g.,
ion, 1988, Pharnz. Res. 5: 539-549). To this end, the oligonucleotide may be
conjugated to
another molecule, e.g., a peptide, a hybridization triggered cross-linking
agent, a transport
agent, a hybridization-triggered cleavage agent, etc.
4.5 I3~STS
The present invention further provides host cells genetically engineered to
contain
the polynucleotides of the invention. For example, such host cells may contain
nucleic acids
of the invention introduced into the host cell using known transformation,
transfection or
infection methods. The present invention still further provides host cells
genetically
engineered to express the polynucleotides of the invention, wherein such
polynucleotides are
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28
in operative association with a regulatory sequence heterologous to the host
cell which
drives expression of the polynucleotides in the cell.
Knowledge of nucleic acid sequences allows for modification of cells to
permit, or
increase, expression of endogenous polypeptide. Cells can be modified (e.g.,
by
homologous recombination) to provide increased polypeptide expression by
replacing, ~in
whole or in part, the naturally occurring promoter with all or part of a
heterologous promoter
so that the cells express the polypeptide at higher levels. The heterologous
promoter is
inserted in such a manner that it is operatively linked to the encoding
sequences. See, for
example, PCT International Publication No. W094/12650, PCT International
Publication
No. W092/20808, and PCT International Publication No. W091/09955. It is also
contemplated that, in addition to heterologous promoter DNA, amplifiable
marker DNA
(e.g., ada, dhfr, and the multifunctional CAD gene which encodes carbamyl
phosphate
synthase, aspartate transcarbamylase, and dihydroorotase) and/or intron DNA
may be
inserted along with the heterologous promoter DNA. If linked to the coding
sequence,
amplification of the marker DNA by standard selection methods results in co-
amplification
of the desired protein coding sequences in the cells.
The host cell can be a higher eukaryotic host cell, such as a mammalian cell,
a lower
eukaryotic host cell, such as a yeast cell, or the host cell can be a
prokaryotic cell, such as a
bacterial cell. Introduction of the recombinant construct into the host cell
can be effected by
calcium ph~sphate transfection, DEAF, dextran mediated transfection, or
electroporation
(Davis, L. et al., B~asie 111rIletla~ds ifi. ll~l~leeulcz,- Bi~l~,~~ (1986)).
The host cells containing one
of the polynucleotides of the inventi~n, can be used in conventional manners
to produce the
gene product encoded by the isolated fragment (in the case of an OI2F) or can
be used to
produce a heterologous protein under the control of the EMF.
Any host/vector system can be used to express one or more of the ORFs of the
present invention. These include, but are not limited to, eukaryotic hosts
such as HeLa cells,
Cv-1 cell, COS cells, 293 cells, and Sf~ cells, as well as prokaryotic host
such as E. coli and
B. subtilis. The most preferred cells are those which d~ not normally express
the particular
polypeptide or protein or which expresses the polypeptide or protein at low
natural level.
Mature proteins can be expressed in mammalian cells, yeast, bacteria, or other
cells under
the control of appropriate promoters. Cell-free translation systems can also
be employed to
produce such proteins using RNAs derived from the DNA constructs of the
present
invention. Appropriate cloning and expression vectors for use with prokaryotic
and
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29
eukaryotic hosts are described by Sambrook, et al., in Molecular Cloning: A
Laboratory
Manual, Second Edition, Cold Spring Harbor, New York (1989), the disclosure of
which is
hereby incorporated by reference.
Various mammalian cell culture systems can also be employed to express
recombinant protein. Examples of mammalian expression systems include the COS-
7 lines
of monkey kidney fibroblasts, described by Gluzman, Cell 23:175 (1981). Other
cell lines
capable of expressing a compatible vector are, for example, the C127, monkey
COS cells,
Chinese Hamster Ovary (CHO) cells, human kidney 293 cells, human epidermal
A431 cells,
human Co1o205 cells, 3T3 cells, CV-1 cells, other transformed primate cell
lines, normal
diploid cells, cell strains derived from in vitro culture of primary tissue,
primary explants,
HeLa cells, mouse L cells, BHK, HL-60, U937, HaK or Jurkat cells. Mammalian
expression
vectors will comprise an origin of replication, a suitable promoter and also
any necessary
ribosome binding sites, polyadenylation site, splice donor and acceptor sites,
transcriptional
termination sequences, and 5 ° flanking nontranscribed sequences. DNA
sequences derived
from the SV40 viral genome, for example, SV40 origin, early promoter,
enhancer, splice,
and polyadenylation sites may be used to provide the required nontranscribed
genetic
elements. Recombinant polypeptides and proteins produced in bacterial culture
are usually
isolated by initial extraction fiom cell pellets, followed by one or more
saltinb out, aqueous
ion exchange or size exclusion chromatography steps. Protein refolding steps
can be used,
as necessary, in completing configuration of the mature protein. Finally, high
performance
liquid chr~matography (HPLC) can be employed for final purification steps.
Micr~bial cells
empl~yed in expression of proteins can be disrupted by any convenient method,
including
freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing
agents.
Alternatively, it may be possible to produce the protein in lower eukaryotes
such as
yeast or insects or in prokaryotes such as bacteria. Potentially suitable
yeast strains include
Sczeclzai~~nayces cerevisiae, Selziz~sacchaYOrnyces ponabe, Kluyveromyces
strains, Candida,
or any yeast strain capable of expressing heterologous proteins. Potentially
suitable bacterial
strains include Escher~ichia coli, Bacillus subtilis, S'alm~nella
yphinaur~ium, or any bacterial
strain capable of expressing heterologous proteins. If the protein is made in
yeast or
bacteria, it may be necessary to modify the protein produced therein, for
example by
phosphorylation or glycosylation of the appropriate sites, in order to obtain
the functional
protein. Such covalent attachments may be accomplished using known chemical or
enzymatic methods.
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In another embodiment of the present invention, cells and tissues may be
engineered
to express an endogenous gene comprising the polynucleotides of the invention
under the
control of inducible regulatory elements, in which case the regulatory
sequences of the
endogenous gene may be replaced by homologous recombination. As described
herein, gene
5 targeting can be used to replace a gene's existing regulatory region with a
regulatory
sequence isolated from a different gene or a novel regulatory sequence
synthesized by
genetic engineering methods. Such regulatory sequences may be comprised of
promoters,
enhancers, scaffold-attachment regions, negative regulatory elements,
transcriptional
initiation sites, and regulatory protein binding sites or combinations of said
sequences.
10 Alternatively, sequences which affect the structure or stability of the RNA
or protein
produced may be replaced, removed, added, or otherwise modified by targeting.
These
sequence include polyadenylation signals, mRNA stability elements, splice
sites, leader
sequences for enhancing or modifying transport or secretion properties of the
protein, or
other sequences which alter or improve the function or stability of protein or
RNA
15 molecules.
The targeting event may be a simple insertion of the regulatory sequence,
placing the
gene under the contr~1 of the new regulatory sequence, e.g., inserting a new
promoter or
enhances or both upstream of a gene. Alternatively, the targeting event may be
a simple
deletion of a regulatory element, such as the deletion of a tissue-specific
negative regulatory
20 element. Alternatively, the targeting event may replace an existing
element; for example, a
tissue-specific enhances can be replaced by an enhances that has broader or
different
cell-type speci~acity than the naturally occurring elements. Here, the
naturally occurring
sequences are deleted and new sequences are added. In all cases, the
identification of the
targeting event may be facilitated by the use of one or more selectable marker
genes that are
25 contiguous with the targeting DNA, allowing for the selection of cells in
which the
exogenous DNA has integrated into the host cell genome. The identification of
the targeting
event may also be facilitated by the use of one or more marker genes
exhibiting the property
of negative selection, such that the negatively selectable marker is linked to
the exogenous
DNA, but configured such that the negatively selectable marker flanks the
targeting
30 sequence, and such that a correct homologous recombination event with
sequences in the
host cell genome does not result in the stable integration of the negatively
selectable marker.
Markers useful for this purpose include the Herpes Simplex Virus thymidine
kinase (TK)
gene or the bacterial xanthine-guanine phosphoribosyl-transferase (gpt) gene.
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31
The gene targeting or gene activation techniques which can be used in
accordance
with this aspect of the invention are more particularly described in U.S.
Patent No. 5,272,071
to Chappel; U.S. Patent No. 5,578,461 to Sherwin et al.; International
Application No.
PCT/LTS92/09627 (W093/09222) by Selden et al.; and International Application
No.
PCT/US90/06436 (W091/06667) by Skoultchi et al., each of which is incorporated
by
reference herein in its entirety.
4.6 POLYPEPTIDES OF THE INVENTION
The isolated polypeptides of the invention include, but are not limited to, a
polypeptide comprising: the amino acid sequences set forth as any one of SEQ
ID NO: 685-
1368, or 1967-2564 or an amino acid sequence encoded by any one of the
nucleotide
sequences SEQ ID NO: 1-684, or 1369-1966 or the corresponding full length or
mature
protein. Polypeptides of the invention also include polypeptides preferably
with biological or
immunological activity that are encoded by: (a) a polynucleotide having any
one of the
nucleotide sequences set forth in SEQ ID NO: 1-684, or 1369-1966 or (b)
polynucleotides
encoding any one of the amino acid sequences set forth as SEQ ID NO: 685-1368,
or 1967-
2564 or (c) polynucleotides that hybridize to the complement of the
polynucleotides of either
(a) or (b) under stringent hybridization conditions. The invention also
provides biologically
active or immunologically active variants of any of the amino acid sequences
set forth as
SEQ ID NO: 685-1368, or 1967-2564 or the corresponding full length or mature
protein; and
"substantial equivalents" thereof (e.g., with at least about
65°A°, at least about 70°/~, at least
about 75°/~, at least about 80%, at least about 85°/~,
86°/~, 87°!~, 88°d°, 89°/~, at least about
90%, 91%, 92%, 93°f°, 94°~°, typically at least
about 95°f°, 96%, 97°J°, more typically at least
about 98%, or most typically at least about 99% amino acid identity) that
retain biological
activity. Polypeptides encoded by allelic variants may have a similar,
increased, or
decreased activity compared to polypeptides comprising SEQ ID NO: 685-1368, or
1967-
2564.
Fragments of the proteins of the present invention which are capable of
exhibiting
biological activity are also encompassed by the present invention. Fragments
of the protein
may be in linear form or they may be cyclized using known methods, for
example, as
described in H. U. Saragovi, et al., Bio/Technology 10, 773-778 (1992) and in
R. S.
McDowell, et al., J. Amer. Chem. Soc. 114, 9245-925'3 (1992), both of which
are
incorporated herein by reference. Such fragments may be fused to carrier
molecules such as
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32
immunoglobulins for many purposes, including increasing the valency of protein
binding
sites. Fragments are also identified in Tables 3A, 3B, 5, 7, or 8.
The present invention also provides both full-length and mature forms (for
example,
without a signal sequence or precursor sequence) of the disclosed proteins.
The protein
coding sequence is identified in the sequence listing by translation of the
disclosed
nucleotide sequences. The predicted signal sequence is set forth in Table 5.
The mature
form of such protein may be obtained and confirmed by expression of a full-
length
polynucleotide in a suitable mammalian cell or other host cell and sequencing
of the cleaved
product. One of skill in the art will recognize that the actual cleavage site
may be different
than that predicted in Table 5. The sequence of the mature form of the protein
is also
determinable from the amino acid sequence of the full-length form. Where
proteins of the
present invention are membrane bound, soluble forms of the proteins are also
provided. In
such forms, part or all of the regions causing the proteins to be membrane
bound are deleted
so that the proteins are fully secreted from the cell in which they are
expressed (See, e.g.,
Sakal et al., Prep. Biochem. Biotechnol. (2000), 30(2), pp. 107-23,
incorporated herein by
reference).
Protein compositions of the present invention may further comprise an
acceptable
carrier, such as a hydrophilic, e.g., pharmaceutically acceptable, carrier.
The present invention further provides isolated polypeptides encoded by the
nucleic
acid fragments of the present invention or by degenerate variants of the
nucleic acid
fragments of the present invention. By "degenerate variant" is intended
nucleotide
fragments which differ from a nucleic acid fragment of the present invention
(e.g., an OHF)
by nucleotide sequence but, due to the degeneracy of the genetic code, encode
an identical
polypeptide sequence. Preferred nucleic acid fragments of the present
invention are the
ORFs that encode proteins.
A variety of methodologies known in the art can be utilized to obtain any one
of the
isolated polypeptides or proteins of the present invention. At the simplest
level, the amino
acid sequence can be synthesized using commercially available peptide
synthesizers. The
synthetically-constructed protein sequences, by virtue of sharing primary,
secondary or
tertiary structural and/or conformational characteristics with proteins may
possess biological
properties in common therewith, including protein activity. This technique is
particularly
useful in producing small peptides and fragments of larger polypeptides.
Fragments are
useful, for example, in generating antibodies against the native polypeptide.
Thus, they may
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33
be employed as biologically active or immunological substitutes for natural,
purified
proteins in screening of therapeutic compounds and in immunological processes
for the
development of antibodies. .
The polypeptides and proteins of the present invention can alternatively be
purred
from cells which have been altered to express the desired polypeptide or
protein. As used
herein, a cell is said to be altered to express a desired polypeptide or
protein when the cell,
through genetic manipulation, is made to produce a polypeptide or protein
which it normally
does not produce or which the cell normally produces at a lower level. One
skilled in the art
can readily adapt procedures for introducing and expressing either recombinant
or synthetic
sequences into eukaryotic or prokaryotic cells in order to generate a cell
which produces one
of the polypeptides or proteins of the present invention.
The invention also relates to methods for producing a polypeptide comprising
growing a culture of host cells of the invention in a suitable culture medium,
and purifying
the protein from the cells or the culture in which the cells are grown. For
example, the
methods of the invention include a process for producing a polypeptide in
which a host cell
containing a suitable expression vector that includes a polynucleotide of the
invention is
cultured under conditions that allow expression of the encoded polypeptide.
The
polypeptide can be recovered from the culture, conveniently from the culture
medium, or
from a lysate prepared from the host cells and further purified. Preferred
embodiments
include those in which the protein produced by such process is a full length
or mature form
of the protein.
In an alternative method, the polypeptide or protein is purified from
bacterial cells
which naturally produce the polypeptide or protein. One skilled in the art can
readily follow
known methods for isolating polypeptides and proteins in order to obtain one
of the isolated
polypeptides or proteins of the present invention. These include, but are not
limited to,
immunochromatography, HPLC, size-exclusion chromatography, ion-exchange
chromatography, and immuno-affinity chromatography. See, e.g~., Scopes,
Proteifa
Purification: Principles arad Pf°actice, Springer-Verlag (1994);
Sambrook, et al., in
Molecular Cloning: A Labof°ato~y Manual; Ausubel et al., Current
Pi°otocols in Molecular
Biology. Polypeptide fragments that retain biological/immunological activity
include
fragments comprising greater than about 100 amino acids, or greater than about
200 amino
acids, and fragments that encode specific protein domains.
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34
The purified polypeptides can be used in in vitro binding assays which are
well
known in the art to identify molecules which bind to the polypeptides. These
molecules
include but are not limited to, for e.g., small molecules, molecules from
combinatorial
libraries, antibodies or other proteins. The molecules identified in the
binding assay are then
tested for antagonist or agonist activity in ira vivo tissue culture or animal
models that are
well known in the art. In brief, the molecules are titrated into a plurality
of cell cultures or
animals and then tested for either cell/animal death or prolonged survival of
the animal/cells.
In addition, the peptides of the invention or molecules capable of binding to
the
peptides may be complexed with toxins, e.g., ricin or cholera, or with other
compounds that
are toxic to cells. The toxin-binding molecule complex is then targeted to a
tumor or other
cell by the specificity of the binding molecule for SEQ ID NO: 685-1368, or
1967-2564.
The protein of the invention may also be expressed as a product of transgenic
animals, e.g., as a component of the milk of transgenic cows, goats, pigs, or
sheep which are
characterized by somatic or germ cells containing a nucleotide sequence
encoding the
protein.
The proteins provided herein also include proteins characterized by amino acid
sequences similar to those of purified proteins but lllto which modification
are naturally
provided or deliberately engineered. For example, modifications, in the
peptide or DNA
sequence, can be made by those skilled in the art using laiown techniques.
Modifications of
interest in the protein sequences may include the alteration, substitution,
replacement,
insertion or deletion of a selected amino acid residue in the coding sequence.
For example,
one or more of the cysteine residues may be deleted or replaced with another
amino acid to
alter the conformation of the molecule. Techniques for such alteration,
substitution,
replacement, insertion or deletion are well known to those skilled in the art
(see, e.g., U.S.
Pat. No. 4,518,584). Preferably, such alteration, substitution, replacement,
insertion or
deletion retains the desired activity of the protein. Regions of the protein
that are important
for the protein function can be determined by various methods known in the art
including the
alanine-scanning method which involved systematic substitution of single or
strings of
amino acids with alanine, followed by testing the resulting alanine-containing
variant for
biological activity. This type of analysis determines the importance of the
substituted amino
acids) in biological activity. Regions of the protein that are important for
protein function
may be determined by the eMATRIX program.
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Other fragments and derivatives of the sequences of proteins which would be
expected to retain protein activity in whole or in part and are useful for
screening or other
imrnunological methodologies may also be easily made by those skilled in the
art given the
disclosures herein. Such modifications are encompassed by the present
invention.
The protein may also be produced by operably linking the isolated
polynucleotide of
the invention to suitable control sequences in one or more insect expression
vectors, and
employing an insect expression system. Materials and methods for
baculovirus/insect cell
expression systems are commercially available in kit form from, e.g.,
Invitrogen, San Diego,
Cali~, U.S.A. (the MaxBatTM kit), and such methods are well known in the art,
as described
10 in Summers and Smith, Texas Agricultural Experiment Station Bulletin No.
1555 (1987),
incorporated herein by reference. As used herein, an insect cell capable of
expressing a
polynucleotide of the present invention is "transformed."
The protein of the invention may be prepared by culturing transformed host
cells
under culture conditions suitable to express the recombinant protein. The
resulting
15 expressed protein may then be purified from such culture (i.e., from
culture medium or cell
extracts) using known purification processes, such as gel filtration and ion
exchange
chromatography. The purification of the protein may also include an affinity
column
containing agents which will bind to the protein, one or more column steps
over such affinity
resins as concanavalin A-agarose, heparin-toyopearlTM or Cibacrom blue 3GA
SepharoseTM;
20 one or more steps involving hydrophobic interaction chromatography using
such resins as
phenyl ether, butyl ether, or propyl ethers or nnmunoafBmtg, chromatography.
Altea-natively, the protein of the invention may also be expressed in a form
which will
facilitate purification. For example, it may be expressed as a fusion protein,
such as those of
maltose binding protein (MBP), glutathione-S-transferase (GST) or thioredoxin
(TRX), or as
25 a His tag. Kits for expression and purification of such fusion proteins are
commercially
available from New England BioLab (Beverly, Mass.), Pharmacia (Piscataway,
N.J.) and
Invitrogen, respectively. The protein can also be tagged with an epitope and
subsequently
purred by using a specific antibody directed to such epitope. One such epitope
("FLAGO")
is commercially available from Kodak (New Haven, Conn.).
30 Finally, one or more reverse-phase high performance liquid chromatography
(RP-
HPLC) steps employing hydrophobic RP-HPLC media, e.g., silica gel having
pendant
methyl or other aliphatic groups, can be employed to further purify the
protein. Some or all
of the foregoing purification steps, in various combinations, can also be
employed to provide
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36
a substantially homogeneous isolated recombinant protein. The protein thus
purified is
substantially free of other mammalian proteins and is defined in accordance
with the present
invention as an "isolated protein."
The polypeptides of the invention include analogs (variants). This embraces
fragments, as well as peptides in which one or more amino acids has been
deleted, inserted,
or substituted. Also, analogs of the polypeptides of the invention embrace
fusions of the
polypeptides or modifications of the polypeptides of the invention, wherein
the polypeptide
or analog is fused to another moiety or moieties, e.g., targeting moiety or
another therapeutic
agent. Such analogs may exhibit improved properties such as activity and/or
stability.
Examples of moieties which may be fused to the polypeptide or an analog
include, for
example, targeting moieties which provide for the delivery of polypeptide to
pancreatic cells,
e.g., antibodies to pancreatic cells, antibodies to immune cells such as T-
cells, monocytes,
dendritic cells, granulocytes, etc., as well as receptor and ligands expressed
on pancreatic or
immune cells. Other moieties which may be fused to the polypeptide include
therapeutic
agents which are used for treatment, for example, immunosuppressive drugs such
as
cyclosporin, SI~506, a~athioprine, CD3 antibodies and steroids. Also,
polypeptides may be
fused to immune modulators, and other cytokines such as alpha or beta
interferon.
4.6.1 DETERMINING POLYPEPT~E AND POLYNiJCLEOTIDE
IDENTITY AND SIMILARITY
Preferred identity and/or similarity are designed to give the largest match
between
the sequences tested. Methods to determine identity and similarity are
codified in computer
programs including, but are not limited to, the GCG program package, including
GAP
(Devereux, J., et al., Nucleic Acids Research 12(1):387 (1984); Genetics
Computer Group,
University of Wisconsin, Madison, WI), BLASTP, BLASTN, BLASTX, FASTA
(Altschul,
S.F. et al., J. Molec. Biol. 215:403-410 (1990), PSI-BLAST (Altschul S.F. et
al., Nucleic
Acids Res. vol. 25, pp. 3389-3402, herein incorporated by reference), eMatrix
software (Wu
et al., J. Comp. Biol., Vol. 6, pp. 219-235 (1999), herein incorporated by
reference), eMotif
software (Nevill-Manning et al, ISMB-97, Vol. 4, pp. 202-209, herein
incorporated by
reference), Pfam software (Sonnhammer et al., Nucleic Acids Res., Vol. 26(1),
pp. 320-322
(1998), herein incorporated by reference) and the I~yte-Doolittle
hydrophobocity prediction
algoritlnn (J. Mol Biol, 157, pp. 105-31 (1982), the GeneAtlas software
(Molecular
Simulations Inc. (MSI), San Diego, CA) (Sanchez and Sali (1998) Proc. Natl.
Acad. Sci., 95,
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37
13597-13602; Kitson DH et al, (2000) "Remote homology detection using
structural
modeling - an evaluation" Submitted; Fischer and Eisenberg (1996) Protein Sci.
5, 947-
955), Neural Network SignalP V1.1 program (from Center for Biological Sequence
Analysis, The Technical University of Denmark) incorporated herein by
reference).
Polypeptide sequences were examined by a proprietary algorithm, SeqLoc that
separates the
proteins into three sets of locales: intracellular, membrane, or secreted.
This prediction is
based upon three characteristics of each polypeptide, including percentage of
cysteine
residues, Kyte-Doolittle scores for the first 20 amino acids of each protein,
and Kyte-
Doolittle scores to calculate the longest hydrophobic stretch of the said
protein. Values of
predicted proteins are compared against the values from a set of 592 proteins
of known
cellular localization from the Swissprot database
(http://www.expasy.ch/sprot). Predictions
are based upon the maximum likelihood estimation.
Pesence of transmembrane regions) was detected using the TMpred program
(http~//www ch embnet.or~/software/TMPRED form.htinl).
The BLAST programs are publicly available from the National Center for
Biotechnology Information (IVCBI) and other sources (BLAST Manual, Altschul,
S., et al.
NCBI NLM NIH Bethesda, MD 20894; Altschul, S., et al., J. Mol. Biol. 215:403-
410
( 1990).
4.7 CHIMERIC AND FUSION PROTEINS
The invention also provides chimeric or fusion proteins. As used herein, a
"chimeric
protein" or "fusion protein" comprises a polypeptide of the invention
operatively linked to
another polypeptide. within a fusion protein the polypeptide according to the
invention can
correspond to all or a portion of a protein according to the invention. In one
embodiment, a
fusion protein comprises at least one biologically active portion of a protein
according to the
invention. In another embodiment, a fusion protein comprises at least two
biologically
active portions of a protein according to the invention. Within the fusion
protein, the term
"operatively linked" is intended to indicate that the polypeptide according to
the invention
and the other polypeptide are fused in-frame to each other. The polypeptide
can be fused to
the N-terminus or C-terminus, or to the middle.
For example, in one embodiment a fusion protein comprises a polypeptide
according
to the invention operably linked to the extracellular domain of a second
protein.
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38
In another embodiment, the fusion protein is a GST-fusion protein in which the
polypeptide sequences of the invention are fused to the C-terminus of the GST
(i.e.,
glutathione S-transferase) sequences.
In another embodiment, the fusion protein is an irnrnunoglobulin fusion
protein in
which the polypeptide sequences according to the invention comprise one or
more domains
fused to sequences derived from a member of the immunoglobulin protein family.
The
immunoglobulin fusion proteins of the invention can be incorporated into
pharmaceutical
compositions and administered to a subject to inhibit an interaction between a
ligand and a
protein of the invention on the surface of a cell, to thereby suppress signal
transduction in
vivo. The immunoglobulin fusion proteins can be used to affect the
bioavailability of a
cognate ligand. Inhibition of the ligand/protein interaction may be useful
therapeutically for
b~th the treatment of proliferative and differentiative disorders, e.g.,
cancer as well as
modulating (e.g., promoting or inhibiting) cell survival. Moreover, the
immunoglobulin
fusion proteins of the invention can be used as irnmunogens to produce
antibodies in a
subject, to purify ligands, and in screening assays to identify molecules that
inhibit the
interacti~n of a polypeptide of the invention with a ligand.
A chimeric or fusion protein of the inventi~n can be produced by standard
recombinant DNA techniques. F'or example, DNA fragments coding for the
different
polypeptide sequences are ligated together in-frame in accordance with
conventional
techniques, e.g., by employing blunt-ended or stagger-ended termini for
ligation, restriction
enzyme digestion to provide for appra~priate termini, filling-in ~f cohesive
ends as
appropriate, alkaline phosphatase treatment t~ avoid undesirable joining, and
enzymatic
ligation. In another emb~diment, the fusion gene can be synthesized by
conventional
techniques including automated DNA synthesizers. Alternatively, PCR
amplification of
gene fragments can be carried out using anchor primers that give rise to
complementary
overhangs between two consecutive gene fragments that can subsequently be
annealed and
reamplified t~ generate a chimeric gene sequence (see, for example, Ausubel et
al. (eds.)
CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Tohn Wiley & Sons, 1992). Moreover,
many expression vectors are commercially available that already encode a
fusion moiety
(e.g., a GST polypeptide). A nucleic acid encoding a polypeptide of the
invention can be
cloned into such an expression vector such that the fusion moiety is linked in-
frame to the
protein of the invention.
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39
4.8 GENE THERAPY
Mutations in the polynucleotides of the invention gene may result in loss of
normal
function of the encoded protein. The invention thus provides gene therapy to
restore normal
activity of the polypeptides of the invention; or to treat disease states
involving polypeptides
of the invention. Delivery of a functional gene encoding polypeptides of the
invention to
appropriate cells is effected ex vivo, in situ, or in vivo by use of vectors,
and more
particularly viral vectors (e.g., adenovirus, adeno-associated virus, or a
retrovirus), or ex vivo
by use of physical DNA transfer methods (e.g., liposomes or chemical
treatments). See, for
example, Anderson, Nature, supplement to vol. 392, no. 6679, pp.25-20 (1998).
For
additional reviews of gene therapy technology see Friedmann, Science, 244:
1275-1281
(1989); Verma, Scientific American: 68-84 (1990); and Miller, Nature, 357: 455-
460 (1992).
Introduction of any one of the nucleotides of the present invention or a gene
encoding the
polypeptides of the present invention can also be accomplished with
extrachromosomal
substrates (transient expression) or artificial chromosomes (stable
expression). Cells may
also be cultured ~ vivo in the presence of proteins of the present invention
in order to
proliferate or to produce a desired effect on or activity in such cells.
Treated cells can then
be introduced in viv~ for therapeutic puaposes. Alternatively, it is
contemplated that in other
human disease states, preventing the expression of or inhibiting the activity
of polypeptides
of the invention will be useful in treating the disease states. It is
contemplated that antisense
therapy or gene therapy could be applied to negatively regulate the expression
of
polypeptides of the invention.
~ther methods inhibiting expression of a protein include the introduction of
antisense
molecules to the nucleic acids of the present invention, their complements, or
their translated
RNA sequences, by methods lrnown in the art. Further, the polypeptides of the
present
invention can be inhibited by using targeted deletion methods, or the
insertion of a negative
regulatory element such as a silencer, which is tissue specific.
The present invention still further provides cells genetically engineered in
vivo to
express the polynucleotides of the invention, wherein such polynucleotides are
in operative
association with a regulatory sequence heterologous to the host cell which
drives expression of
the polynucleotides in the cell. These methods can be used to increase or
decrease the
expression of the polynucleotides of the present invention.
Knowledge of DNA sequences provided by the invention allows for modification
of
cells to permit, increase, or decrease, expression of endogenous polypeptide.
Cells can be
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modified (e.g., by homologous recombination) to provide increased polypeptide
expression by
replacing, in whole or in part, the naturally occurring promoter with all or
part of a heterologous
promoter so that the cells express the protein at higher levels. The
heterologous promoter is
inserted in such a manner that it is operatively linked to the desired protein
encoding sequences.
5 See, for example, PCT International Publication No. WO 94/12650, PCT
International
Publication No. WO 92/20808, and PCT International Publication No. WO
91/09955. It is also
contemplated that, in addition to heterologous promoter DNA, amplifiable
marker DNA (e.g.,
ada, dhfr, and the multifunctional CAD gene which encodes carbamyl phosphate
synthase,
aspartate transcarbamylase, and dihydroorotase) and/or intron DNA may be
inserted along with
10 the heterologous promoter DNA. If linked to the desired protein coding
sequence,
amplification of the marker DNA by standard selection methods results in co-
amplification of
the desired protein coding sequences in the cells.
In another embodiment of the present invention, cells and tissues may be
engineered to
express an endogenous gene comprising the polynucleotides of the invention
under the control
15 of inducible regulatory elements, in which case the regulatory sequences of
the endogenous
gene may be replaced by homologous recombination. As described herein, gene
targeting can
be used to replace a gene's existing regulatory region with a regulatory
sequence isolated from
a different gene or a n~vel regulatory sequence synthesized by genetic
engineering methods.
Such regulatory sequences may be comprised of promoters, enhancers, scaffold-
attachment
20 regions, negative regulatory elements, transcriptional initiation sites,
regulatory protein binding
sites or combinations of said sequences. Alternatively, sequences which affect
the structure or
stability of the RNA or protein produced may be replaced, removed9 added9 or
otherwise
modified by targeting. These sequences include polyadenylation signals, mRNA
stability
elements, splice sites, leader sequences for enhancing or modifying transport
or secretion
25 properties of the protein, or other sequences which alter or improve the
function or stability of
protein or RNA molecules.
The targeting event may be a simple insertion of the regulatory sequence,
placing the
gene under the control of the new regulatory sequence, e.g., inserting a new
promoter or
enhancer or both upstream of a gene. Alternatively, the targeting event may be
a simple
30 deletion of a regulatory element, such as the deletion of a tissue-specific
negative regulatory
element. Alternatively, the targeting event may replace an existing element;
for example, a
tissue-specific enhancer can be replaced by an enhancer that has broader or
different cell-type
specificity than the naturally occurnng elements. Here, the naturally
occurring sequences are
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41
deleted and new sequences are added. In all cases, the identification of the
targeting event may
be facilitated by the use of one or more selectable marker genes that are
contiguous with the
targeting DNA, allowing for the selection of cells in which the exogenous DNA
has integrated
into the cell genome. The identification of the targeting event may also be
facilitated by the use
of one or more marker genes exhibiting the property of negative selection,
such that the
negatively selectable marker is linked to the exogenous DNA, but configured
such that the
negatively selectable marker flanks the targeting sequence, and such that a
correct homologous
recombination event with sequences in the host cell genome does not result in
the stable
integration of the negatively selectable marker. Markers useful for this
purpose include the
Herpes Simplex Virus thymidine kinase (TK) gene or the bacterial xanthine-
guanine
phosphoribosyl-transferase (gpt) gene.
The gene targeting or gene activation techniques which can be used in
accordance with
this aspect of the invention are more particularly described in U.S. Patent
No. 5,272,071 to
Chappel; U.S. Patent No. 5,578,461 to Sherwin et al.; International
Application No.
PCT/LTS92/09627 (WO93/09222) by Selden et al.; and International Application
No.
PCT/LTS90/06436 (WO91/06667) by Skoultchi et al., each of which is
incorporated by
reference herein in its entirety.
4.9 TRA1VSGE1VIC ANI1V1ALS
In preferred methods to determine biological functions of the polypeptides of
the
invention in vivo, one or more genes provided by the invention are either over
expressed or
inactivated in the germ line of animals using homologous recombination
[Capecchi, Science
244:1288-1292 (1989)]. Animals in which the gene is over expressed, under the
regulatory
control of exogenous or endogenous promoter elements, are known as transgenic
animals.
Animals in which an endogenous gene has been inactivated by homologous
recombination
are referred to as "knockout" animals. Knockout animals, preferably non-human
mammals,
can be prepared as described in U.S. Patent No. 5,557,032, incorporated herein
by reference.
Transgenic animals are useful to determine the roles polypeptides of the
invention play in
biological processes, and preferably in disease states. Transgenic animals are
useful as model
systems to identify compounds that modulate lipid metabolism. Transgenic
animals,
preferably non-human mammals, are produced using methods as described in U.S.
Patent No
5,489,743 and PCT Publication No. W094/28122, incorporated herein by
reference.
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42
Transgenic animals can be prepared wherein all or part of a promoter of the
polynucleotides of the invention is either activated or inactivated to alter
the level of
expression of the polypeptides of the invention. Inactivation can be carried
out using
homologous recombination methods described above. Activation can be achieved
by
supplementing or even replacing the homologous promoter to provide for
increased protein
expression. The homologous promoter can be supplemented by insertion of one or
more
heterologous enhancer elements known to confer promoter activation in a
particular tissue.
The polynucleotides of the present invention also make possible the
development,
through, e.g., homologous recombination or knock out strategies, of animals
that fail to
express polypeptides of the invention or that express a variant polypeptide.
Such animals are
useful as models for studying the iia vivo activities of polypeptide as well
as for studying
modulators of the polypeptides of the invention.
In preferred methods to determine biological functions of the polypeptides of
the
invention ift. vivo, one or more genes provided by the invention are either
over expressed or
inactivated in the germ line of animals using homologous recombination
[Capecchi, Science
244:1288-1292 (1989)x. Animals in which the gene is over expressed, under the
regulatory
control of exogenous or endogenous promoter elements, are known as transgenic
animals.
Animals in which an endogenous gene has been inactivated by homologous
recombination
are referred to as "knockout" animals. IW ockout animals, preferably non-human
mammals,
can be prepared as described in U.S. Patent No. 5,557,032, incorporated herein
by reference.
Transgenic animals are useful to determine the roles polypeptides of the
invention play in
biological processes, and preferably in disease states. Transgenic animals are
useful as model
systems to identify compounds that modulate lipid metabolism. Transgenic
animals,
preferably non-human mammals, are produced using methods as described in U.S.
Patent No
5,489,743 and PCT Publication No. W094/28122, incorporated herein by
reference.
Transgenic animals can be prepared wherein all or part of the polynucleotides
of the
invention promoter is either activated or inactivated to alter the level of
expression of the
polypeptides of the invention. Inactivation can be carried out using
homologous
recombination methods described above. Activation can be achieved by
supplementing or
even replacing the homologous promoter to provide for increased protein
expression. The
homologous promoter can be supplemented by insertion of one or more
heterologous
enhancer elements known to confer promoter activation in a particular tissue.
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43
4.10 USES AND BIOLOGICAL ACTIVITY
The polynucleotides and proteins of the present invention are expected to
exhibit one
or more of the uses or biological activities (including those associated with
assays cited
herein) identified herein. Uses or activities described for proteins of the
present invention
may be provided by administration or use of such proteins or of
polynucleotides encoding
such proteins (such as, for example, in gene therapies or vectors suitable for
introduction of
DNA). The mechanism underlying the particular condition or pathology will
dictate whether
the polypeptides of the invention, the polynucleotides of the invention or
modulators
(activators or inhibitors) thereof would be beneficial to the subject in need
of treatment.
Thus, "therapeutic compositions of the invention" include compositions
comprising isolated
polynucleotides (including recombinant DNA molecules, cloned genes and
degenerate
variants thereof) or polypeptides of the invention (including full length
protein, mature
protein and truncations or domains thereof), or compounds and other substances
that
modulate the overall activity of the target gene products, either at the level
of target
gene/protein expression or target protein activity. Such modulators include
polypeptides,
analogs, (variants), including fragments and fusion proteins, antibodies and
other binding
proteins; chemical compounds that directly or indirectly activate or inhibit
the polypeptides
of the invention (identified, e.g., via drug screening assays as described
herein); antisense
polynucleotides and polynucleotides suitable for triple helix formation; and
in particular
antibodies or other binding partners that specifically recognize one or more
epitopes of the
polypeptides of the invention.
The polypeptides of the present invention may likewise be involved in cellular
activation or in one of the other physiological pathways described herein.
4.10.1 RESEARCH USES AND UTILITIES
The polynucleotides provided by the present invention can be used by the
research
conununity for various purposes. The polynucleotides can be used to express
recombinant
protein for analysis, characterization or therapeutic use; as markers for
tissues in which the
corresponding protein is preferentially expressed (either constitutively or at
a particular stage
of tissue differentiation or development or in disease states); as molecular
weight markers on
gels; as chromosome markers or tags (when labeled) to identify chromosomes or
to map
related gene positions; to compare with endogenous DNA sequences in patients
to identify
potential genetic disorders; as probes to hybridize and thus discover novel,
related DNA
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44
sequences; as a source of information to derive PCR primers for genetic
fingerprinting; as a
probe to "subtract-out" known sequences in the process of discovering other
novel
polynucleotides; for selecting and making oligomers for attachment to a "gene
chip" or other
support, including for examination of expression patterns; to raise anti-
protein antibodies
using DNA immunization techniques; and as an antigen to raise anti-DNA
antibodies or
elicit another immune response. Where the polynucleotide encodes a protein
which binds or
potentially binds to another protein (such as, for example, in a receptor-
ligand interaction),
the polynucleotide can also be used in interaction trap assays (such as, for
example, that
described in Gyuris et al., Cell 75:791-803 (1993)) to identify
polynucleotides encoding the
other protein with which binding occurs or to identify inhibitors of the
binding interaction.
The polypeptides provided by the present invention can similarly be used in
assays to
determine biological activity, including in a panel of multiple proteins for
high-throughput
screening; to raise antibodies or to elicit another immune response; as a
reagent (including
the labeled reagent) in assays designed to quantitatively determine levels of
the protein (or
its receptor) in biological fluids; as markers for tissues in which the
corresponding
polypeptide is preferentially expressed (either constitutively or at a
particular stage of tissue
differentiation or development or in a disease state); and, of course, to
isolate correlative
receptors or ligands. Proteins involved in these binding interactions can also
be used to
screen for peptide or small molecule inhibitors or agonists of the binding
interaction.
Any or all of these research utilities are capable of being developed into
reagent
grade or kit format for coanmercialization as research products.
Methods for performing the uses listed above are well knov~m to those skilled
in the
art. References disclosing such methods include without limitation "Molecular
Cloning: A
Laboratory Manual", 2d ed., Cold Spring Harbor Laboratory Press, Sambrook, J.,
E. F.
Fritsch and T. Maniatis eds., 1989, and "Methods in Enzymology: Guide to
Molecular
Cloning Techniques", Academic Press, Bergen S. L. and A. R. I~immel eds.,
1987.
4.10.2 NUTRITIONAL USES
Polynucleotides and polypeptides of the present invention can also be used as
nutritional sources or supplements. Such uses include without limitation use
as a protein or
amino acid supplement, use as a carbon source, use as a nitrogen source and
use as a source of
carbohydrate. In such cases the polypeptide or polynucleotide of the invention
can be added to
the feed of a particular organism or can be administered as a separate solid
or liquid
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preparation, such as in the form of powder, pills, solutions, suspensions or
capsules. In the case
of microorganisms, the polypeptide or polynucleotide of the invention can be
added to the
medium in or on which the microorganism is cultured.
4.10.3 CYTOKINE AND CELL PROLIFERATION/DIFFERENTIATION
ACTIVITY
A polypeptide of the present invention may exhibit activity relating to
cytokine, cell
proliferation (either inducing or inhibiting) or cell differentiation (either
inducing or
inhibiting) activity or may induce production of other cytokines in certain
cell populations.
10 A polynucleotide of the invention can encode a polypeptide exhibiting such
attributes.
Many protein factors discovered to date, including all known cytokines, have
exhibited
activity in one or more factor-dependent cell proliferation assays, and hence
the assays serve
as a convenient confirmation of cytokine activity. The activity of therapeutic
compositions
of the present invention is evidenced by any one of a number of routine factor
dependent cell
15 proliferation assays for cell lines including, without limitation, 32D,
DA2, DA1G, T10, B9,
B9/11, BaF3, MC9lG, M+(preB M+), 2E8, RBS, DA1, 123, T1165, HT2, CTLL2, TF-1,
Mo7e, CMI~, HUVEC, and Cac~. Therapeutic compositi~ns of the invention can be
used in
the following:
Assays for T-cell or thymocyte proliferation include without limitation those
20 described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M.
I~ruisbeek, D. H.
Margulies, E. M. Shevach, W. Strobes, Pub. Greene Publishing Associates and
Wiley-Interscience (Chapter 3, Iya T~a~a~~ assays for Mouse Lymphocyte
Function 3.1-3.19;
Chapter 7, Immunol~gic studies in Humans); Takai et al., J. Immunol. 137:3494-
3500, 1986;
Bertagnolli et al., J. Immunol. 145:1706-1712, 1990; Bertagnolli et al.,
Cellular Immunology
25 133:327-341, 1991; Bertagnolli, et al., I. Immunol. 149:3778-3783, 1992;
Bowman et al., I.
Immunol. 152:1756-1761, 1994.
Assays for cytokine production and/or proliferation of spleen cells, lymph
node cells
or thymocytes include, without limitation, those described in: Polyclonal T
cell stimulation,
Kruisbeek, A. M. and Shevach, E. M. In Current Protocols in Immunology. J. E.
e.a. Coligan
30 eds. Vol 1 pp. 3.12.1-3.12.14, John Wiley and Sons, Toronto. 1994; and
Measurement of
mouse and human interleukin-y, Schreiber, R. D. In Current Protocols in
Immunology. J. E.
e.a. Coligan eds. Vol 1 pp. 6.8.1-6.8.8, Jolm Wiley and Sons, Toronto. 1994.
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46
Assays for proliferation and differentiation of hematopoietic and
lyrnphopoietic cells
include, without limitation, those described in: Measurement of Human and
Murine
Interleukin 2 and Interleukin 4, Bottomly, K., Davis, L. S. and Lipsky, P. E.
In Current
Protocols in Immunology. J. E. e.a. Coligan eds. Vol 1 pp. 6.3.1-6.3.12, John
Wiley and
Sons, Toronto. 1991; deVries et al., J. Exp. Med. 173:1205-1211, 1991; Moreau
et al.,
Nature 336:690-692, 1988; Greenberger et al., Proc. Natl. Acad. Sci. U.S.A.
80:2931-2938,
1983; Measurement of mouse and human interleukin 6--Nordan, R. In Current
Protocols in
Immunology. J. E. Coligan eds. Vol 1 pp. 6.6.1-6.6.5, John Wiley and Sons,
Toronto. 1991;
Smith et al., Proc. Natl. Aced. Sci. U.S.A. 83:1857-1861, 1986; Measurement of
human
Interleukin 11--Bennett, F., Giannotti, J., Clark, S. C. and Turner, K. J. In
Current Protocols
in Immunology. J. E. Coligan eds. Vol 1 pp. 6.15.1 John Wiley and Sons,
Toronto. 1991;
Measurement of mouse and human Interleukin 9--Ciarletta, A., Giannotti, J.,
Clark, S. C.
and Turner, K. J. In Current Protocols in Immunology. J. E. Coligan eds. Vol 1
pp. 6.13.1,
John Wiley and Sons, Toronto. 1991.
Assays for T-cell clone responses to antigens (which will identify, among
others,
proteins that affect APC-T cell interactions as well as direct T-cell effects
by measuring
proliferation and cytokine production) include, without limitation, those
described in:
Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Krnisbeek, D. H.
Margulies,
E. M. Shevach, W Strober, Pub. Greene Publishing Associates and Wiley-
Interscience
(Chapter 3, In Vitro assays for Mouse Lymphocyte Function; Chapter 6,
Cytokines and their
cellular receptors; Chapter 7, Immunologic studies in humans); Weinberger et
al., Proc.
Natl. Acad. Sci. USA 77:6091-6095, 1980; Weinberger et al., Eur. J. Immun.
11:405-411,
1981; Takai et al., J. Immunol. 137:3494-3500, 1986; Takai et al., J. Immunol.
140:508-512,
1988.
4.10.4 STEM CELL GROWTH FACTOR ACTIVITY
A polypeptide of the present invention may exhibit stem cell growth factor
activity
and be involved in the proliferation, differentiation and survival of
pluripotent and totipotent
stem cells including primordial germ cells, embryonic stem cells,
hematopoietic stem cells
andlor germ line stem cells. Administration of the polypeptide of the
invention to stem cells
ira vivo or ex vivo is expected to maintain and expand cell populations in a
totipotential or
pluripotential state which would be useful for re-engineering damaged or
diseased tissues,
transplantation, manufacture of bio-pharmaceuticals and the development of bio-
sensors.
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47
The ability to produce large quantities of human cells has important working
applications for
the production of human proteins which currently must be obtained from non-
human sources
or donors, implantation of cells to treat diseases such as Parkinson's,
Alzheimer's and other
neurodegenerative diseases; tissues for grafting such as bone marrow, skin,
cartilage,
tendons, bone, muscle (including cardiac muscle), blood vessels, cornea,
neural cells,
gastrointestinal cells and others; and organs for transplantation such as
kidney, liver,
pancreas (including islet cells), heart and lung.
It is contemplated that multiple different exogenous growth factors and/or
cytokines
may be administered in combination with the polypeptide of the invention to
achieve the
desired effect, including any of the growth factors listed herein, other stem
cell maintenance
factors, and specifically including stem cell factor (SCF), leukemia
inhibitory factor (LIF),
Flt-3 ligand (Flt-3L), any of the interleukins, recombinant soluble IL-6
receptor fused to IL-
6, macrophage inflammatory protein 1-alpha (MIP-1-alpha), G-CSF, GM-CSF,
thrombopoietin (TPQ), platelet factor 4 (PF-4), platelet-derived growth factor
(PDGF),
neural growth factors and basic fibroblast growth factor (bFGF).
Since totipotent stem cells can give rise to virtually any mature cell type,
expansion
of these cells in culture will facilitate the production of large quantities
of mature cells.
Techniques for culturing stem cells are known in the art and administration of
polypeptides
of the invention, optionally with other growth factors and/or cytokines, is
expected to
enhance the survival and proliferation of the stem cell populations. This can
be
accomplished by direct administration of the polypeptide of the invention to
the culture
medium. Alternatively, stroma cells transfected with a polynucleotide that
encodes for the
polypeptide of the invention can be used as a feeder layer for the stem cell
populations in
culture or in vivo. Stromal support cells for feeder layers rnay include
embryonic bone
marrow fibroblasts, bone marrow stromal cells, fetal liver cells, or cultured
embryonic
fibroblasts (see U.S. Patent No. 5,690,926).
Stem cells themselves can be transfected with a polynucleotide of the
invention to
induce autocrine expression of the polypeptide of the invention. This will
allow for
generation of undifferentiated totipotential/pluripotential stem cell lines
that are useful as is
or that can then be differentiated into the desired mature cell types. These
stable cell lines
can also serve as a source of undifferentiated totipotential/pluripotential
mRNA to create
cDNA libraries and templates for polymerase chain reaction experiments. These
studies
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48
would allow for the isolation and identification of differentially expressed
genes in stem cell
populations that regulate stem cell proliferation and/or maintenance.
Expansion and maintenance of totipotent stem cell populations will be useful
in the
treatment of many pathological conditions. For example, polypeptides of the
present
invention may be used to manipulate stem cells in culture to give rise to
neuroepithelial cells
that can be used to augment or replace cells damaged by illness, autoimmune
disease,
accidental damage or genetic disorders. The polypeptide of the invention may
be useful for
inducing the proliferation of neural cells and for the regeneration of nerve
and brain tissue,
i.e. for the treatment of central and peripheral nervous system diseases and
neuropathies, as
well as mechanical and traumatic disorders which involve degeneration, death
or trauma to
neural cells or nerve tissue. In addition, the expanded stem cell populations
can also be
genetically altered for gene therapy purposes and to decrease host rejection
of replacement
tissues after grafting or implantation.
Expression of the polypeptide of the invention and its effect on stem cells
can also be
manipulated to achieve controlled differentiation of the stem cells into more
differentiated
cell types. A broadly applicable method of obtaining pure populations of a
specific
differentiated cell type from undifferentiated stem cell populations involves
the use of a cell-
type specific promoter driving a selectable marker. The selectable marker
allows only cells
of the desired type to survive. For example, stem cells can be induced to
differentiate into
cardiomyocytes (Wobus et al., Differentiation, 48: 173-182, (1991); Klug et
al., J. Clin.
Invest., 98(1): 216-224, (1998)) or skeletal muscle cells (Erowder, L. V~. In:
Pa-t~eipl~s ~f
Tissue E~z~iraeeF°i~ag- eds. Lanza et al., Academic Press (1997)).
Alternatively, directed
differentiation of stem cells can be accomplished by culturing t1]e stem cells
in the presence
of a differentiation factor such as retinoic acid and an antagonist of the
polypeptide of the
invention which would inhibit the effects of endogenous stem cell factor
activity and allow
differentiation to proceed.
Irr vitro cultures of stem cells can be used to determine if the polypeptide
of the
invention exhibits stem cell growth factor activity. Stem cells are isolated
from any one of
various cell sources (including hematopoietic stem cells and embryonic stem
cells) and
cultured on a feeder layer, as described by Thompson et al. Proc. Natl. Acad.
Sci, U.S.A.,
92: 7844-7848 (1995), in the presence of the polypeptide of the invention
alone or in
combination with other growth factors or cytokines. The ability of the
polypeptide of the
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49
invention to induce stem cells proliferation is determined by colony formation
on semi-solid
support e.g. as described by Bernstein et al., Blood, 77: 2316-2321 (1991).
4.10.5 HEMATOPOIESIS REGULATING ACTIVITY
A polypeptide of the present invention may be involved in regulation of
hematopoiesis and, consequently, in the treatment of myeloid or lymphoid
cell~disorders.
Even marginal biological activity in support of colony forming cells or of
factor-dependent
cell lines indicates involvement in regulating hematopoiesis, e.g. in
supporting the growth
and proliferation of erythroid progenitor cells alone or in combination with
other cytokines,
thereby indicating utility, for example, in treating various anemias or for
use in conjunction
with irradiatioi~/chemotherapy to stimulate the production of erythroid
precursors and/or
erythroid cells; in supporting the growth and proliferation of myeloid cells
such as
granulocytes and monocytes/macrophages (i.e., traditional CSF activity)
useful, for example,
in conjunction with chemotherapy to prevent or treat consequent myelo-
suppression; in
supporting the growth and proliferation of megakaryocytes and consequently of
platelets
thereby allowing prevention or treatment of various platelet disorders such as
thxombocytopenia, and generally for use in place of or complimentary to
platelet
transfusions; and/or in supporting the growth and proliferation of
hematopoietic stem cells
which are capable of maturing to any and all of the above-mentioned
hematopoietic cells and
therefore find therapeutic utility in various stem cell disorders (such as
those usually treated
with transplantation, including, without limitation, aplastic anemia and
paroxysmal nocturnal
hemoglobinuria), as well as in repopulating the stem cell compartment post
irradiationchemotherapy, either ifa-viv~ or ex-viv~ (i.e., in conjunction with
bone marrow
transplantation or with peripheral progenitor cell transplantation (homologous
or
heterologous)) as normal cells or genetically manipulated for gene therapy.
Therapeutic compositions of the invention can be used in the following:
Suitable assays for proliferation and differentiation of various hematopoietic
lines are
cited above.
Assays for embryonic stem cell differentiation (which will identify, among
others,
proteins that influence embryonic differentiation hematopoiesis) include,
without limitation,
those described in: Johansson et al. Cellular Biology 15:141-151, 1995; Keller
et al.,
Molecular and Cellular Biology 13:473-486, 1993; McClanahan et al., Blood
81:2903-2915,
1993.
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Assays for stem cell survival and differentiation (which will identify, among
others,
proteins that regulate lympho-hematopoiesis) include, without limitation,
those described in:
Methylcellulose colony forming assays, Freshney, M. G. In Culture of
Hematopoietic Cells.
R. I. Freshney, et al. eds. Vol pp. 265-268, Wiley-Liss, Inc., New York, N.Y.
1994;
5 Hirayama et al., Proc. Natl. Acad. Sci. USA 89:5907-5911, 1992; Primitive
hematopoietic
colony forming cells with high proliferative potential, McNiece, I. I~. and
Briddell, R. A. In
Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 23-39,
Wiley-Liss, Inc.,
New York, N.Y. 1994; Neben et al., Experimental Hematology 22:353-359, 1994;
Cobblestone area forming cell assay, Ploemacher, R. E. In Culture of
Hematopoietic Cells.
10 R. I. Freshney, et al. eds. Vol pp. 1-21, Wiley-Liss, Inc., New York, N.Y.
1994; Long term
bone marrow cultures in the presence of stromal cells, Spooncer, E., Dexter,
M. and Allen,
T. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 163-
179, Wiley-Liss,
Inc., New York, N.Y. 1994; Long term culture initiating cell assay,
Sutherland, H. J. In
. Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 139-162,
Wiley-Liss, Inc.,
15 New York, N.Y. 1994.
4.10.6 TJSSZTE ~1~~WTH ACTIVITY
A polypeptide of the present invention also may be involved in bone,
cartilage,
tendon, ligament and/or nerve tissue growth or regeneration, as well as in
wound healing and
20 tissue repair and replacement, and in healing of burns, incisions and
ulcers.
A polypeptide of the present invention which induces cartilage and/or bone
growth in
circumstances where bone is not normally formed, has application in the
healing of bone
fractures and cartilage damage or defects in humans and other animals.
Compositions of a
polypeptide, antibody, binding partner, or other modulator of the invention
may have
25 prophylactic use in closed as well as open fracture reduction and also in
the improved
fixation of artificial joints. De novo bone formation induced by an osteogenic
agent
contributes to the repair of congenital, trauma induced, or oncologic
resection induced
craniofacial defects, and also is useful in cosmetic plastic surgery.
A polypeptide of this invention may also be involved in attracting bone-
forming
30 cells, stimulating growth of bone-forming cells, or inducing
differentiation of progenitors of
bone-forming cells. Treatment of osteoporosis, osteoarthritis, bone
degenerative disorders, or
periodontal disease, such as through stimulation of bone and/or cartilage
repair or by
blocking inflammation or processes of tissue destruction (collagenase
activity, osteoclast
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51
activity, etc.) mediated by inflammatory processes may also be possible using
the
composition of the invention.
Another category of tissue regeneration activity that may involve the
polypeptide of
the present invention is tendon/ligament formation. Induction of
tendon/ligament-like tissue
or other tissue formation in circumstances where such tissue is not normally
formed, has
application in the healing of tendon or ligament tears, deformities and other
tendon or
ligament defects in humans and other animals. Such a preparation employing a
tendon/ligament-like tissue inducing protein may have prophylactic use in
preventing
damage to tendon or ligament tissue, as well as use in the improved fixation
of tendon or
ligament to bone or other tissues, and in repairing defects to tendon or
ligament tissue. De
novo tendon/ligament-like tissue formation induced by a composition of the
present
invention contributes to the repair of congenital, trauma induced, or other
tendon or ligament
defects of other origin, and is also useful in cosmetic plastic surgery for
attachment or repair
of tendons or ligaments. The compositions of the present invention may provide
environment to attract tendon- or ligament-fornling cells, stimulate growth of
tendon- or
ligament-forming cells, induce differentiati~n of progenitors of tendon- or
ligament-forming
cells, or induce growth of tendon/ligament cells ~r progenitors ~ vtv~ for
return ih. vav~ t~
effect tissue repair. The compositions of the invention may also be useful in
the treatment ~f
tendinitis, carpal tunnel syndrome and other tendon or ligament defects. The
compositions
may also include an appropriate matrix and/or sequestering agent as a carrier
as is well
kn~wn in the art.
The compositions of the present invention may also be useful for proliferation
~f
neural cells and for regeneration of nerve and brain tissue, i.e. for the
treatment of central
and peripheral nervous system diseases and neuropathies, as well as mechanical
and
traumatic disorders, which involve degeneration, death or trauma to neural
cells or nerve
tissue. More specifically, a composition may be used in the treatment of
diseases of the
peripheral nervous system, such as peripheral nerve injuries, peripheral
neuropathy and
localized neuropathies, and central nervous system diseases, such as
Alzheimer's,
Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and
Shy-Drager
syndrome. Further conditions which may be treated in accordance with the
present invention
include mechanical and traumatic disorders, such as spinal cord disorders,
head trauma and
cerebrovascular diseases such as stroke. Peripheral neuropathies resulting
from
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52
chemotherapy or other medical therapies may also be treatable using a
composition of the
invention.
Compositions of the invention may also be useful to promote better or faster
closure
of non-healing wounds, including without limitation pressure ulcers, ulcers
associated with
vascular insufficiency, surgical and traumatic wounds, and the like.
Compositions of the present invention may also be involved in the generation
or
regeneration of other tissues, such as organs (including, for example,
pancreas, liver,
intestine, kidney, skin, endothelium), muscle (smooth, skeletal or cardiac)
and vascular
(including vascular endothelium) tissue, or for promoting the growth of cells
comprising
such tissues. Part of the desired effects may be by inhibition or modulation
of fibrotic
scarring may allow normal tissue to regenerate. A polypeptide of the present
invention rnay
also exhibit angiogenic activity.
A composition of the present invention may also be useful for gut protection
or
regeneration and treatment of lung or liver fibrosis, reperfusion injury in
various tissues, and
conditions resulting from systemic cytokine damage.
A composition of the present invention may also be useful for promoting or
inhibiting differentiation of tissues described above from precursor tissues
or cells; or for
inhibiting the growth of tissues described above.
Therapeutic compositions of the invention can be used in the following:
Assays for tissue generation activity include, without limitation, those
described in:
International Patent Publication I~To. W~95116035 (bone, cartilage, tendon)e
International
Patent Publication 1'To. W~95/05846 (nerve, neuronal)9 International Patent
Publication IVo.
W~91/07491 (skin, endothelium).
Assays for wound healing activity include, without limitation, those described
in:
Winter, Epidermal Wound Healing, pps. 71-112 (Maibach, H. I. and Rovee, D. T.,
eds.),
Year Book Medical Publishers, Inc., Chicago, as modified by Eaglstein and
Mertz, J. Invest.
Dermatol 71:382-84 (1978).
4.10.7 IMMUNE STIMULATING OR SUPPRESSING ACTIVITY
A polypeptide of the present invention may also exhibit immune stimulating or
immune suppressing activity, including without limitation the activities for
which assays are
described herein. A polynucleotide of the invention can encode a polypeptide
exhibiting
such activities. A protein may be useful in the treatment of various immune
deficiencies and
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53
disorders (including severe combined immunodeficiency (SCID)), e.g., in
regulating (up or
down) growth and proliferation of T and/or B lymphocytes, as well as effecting
the cytolytic
activity of NL cells and other cell populations. These immune deficiencies may
be genetic or
be caused by viral (e.g., HIV) as well as bacterial or fungal infections, or
may result from
autoimmune disorders. More specifically, infectious diseases causes by viral,
bacterial,
fungal or other infection may be treatable using a protein of the present
invention, including
infections by HIV, hepatitis viruses, herpes viruses, mycobacteria, Leishmania
spp., malaria
spp. and various fungal infections such as candidiasis. Of course, in this
regard, proteins of
the present invention may also be useful where a boost to the immune system
generally may
be desirable, i.e., in the treatment of cancer.
Autoimmune disorders which may be treated using a protein of the present
invention
include, for example, connective tissue disease, multiple sclerosis, systemic
lupus
eiythematosus, rheumatoid arthritis, autoimmune pulmonary inflammation,
Guillain-Barre
syndrome, autoimmune thyroiditis, insulin dependent diabetes mellitis,
myasthenia gravis,
graft-versus-host disease and autoimmune inflammatory eye disease. Such a
protein (~r
antagonists thereof, including antib~dies) of the present invention may also
to be useful in
the treatment of allergic reactions and conditions (e.~., anaphylaxis, serum
sickness, drug
reactions, food allergies, insect venom allergies, mastocytosis, allergic
rhinitis,
hypersensitivity pneumonitis, urticaria, angioedema, eczema, atopic
dernlatitis, allergic
contact dermatitis, erythema multiforme, Stevens-Johnson syndrome, allergic
conjunctivitis,
atopic keratoconjunctivitis, venereal keratoconjunctivitis, giant papillary
conjunctivitis and
contact allergies), such as asthma (particularly allergic asthma) or other
respiratory
problems. Other conditions, in which immune suppression is desired (including,
f~r
example, organ transplantation), may also be treatable using a protein (or
antagonists
thereof) of the present invention. The therapeutic effects of the polypeptides
or antagonists
thereof on allergic reactions can be evaluated by in vivo animals models such
as the
cumulative contact enhancement test (Lastbom et al., Toxicology 125: 59-66,
1998), skin
prick test (Hoffmann et al., Allergy 54: 446-54, 1999), guinea pig skin
sensitization test
(Voter et al., Arch. Toxocol. 73: 501-9), and murine local lymph node assay
(Limber et al.,
J. Toxicol. Environ. Health 53: 563-79).
Using the proteins of the invention it may also be possible to modulate immune
responses, in a number of ways. Down regulation may be in the form of
inhibiting or
blocking an immune response already in progress or may involve preventing the
induction of
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54
an immune response. The functions of activated T cells may be inhibited by
suppressing T
cell responses or by inducing specific tolerance in T cells, or both.
Immunosuppression of T
cell responses is generally an active, non-antigen-specific, process which
requires continuous
exposure of the T cells to the suppressive agent. Tolerance, which involves
inducing
non-responsiveness or energy in T cells, is distinguishable from
immunosuppression in that
it is generally antigen-speciftc and persists after exposure to the tolerizing
agent has ceased.
Operationally, tolerance can be demonstrated by the lack of a T cell response
upon
reexposure to specific antigen in the absence of the tolerizing agent.
Down regulating or preventing one or more antigen functions (including without
limitation B lymphocyte antigen functions (such as, for example, B7)), e.g.,
preventing high
level lymphokine synthesis by activated T cells, will be useful in situations
of tissue, skin
and organ transplantation and in graft-versus-host disease (GVHD). For
example, blockage
of T cell function should result in reduced tissue destruction in tissue
transplantation.
Typically, in tissue transplants, rejection of the transplant is initiated
through its recognition
as foreign by T cells, followed by an immune reaction that destroys the
transplant. The
administration of a therapeutic composition of the invention may prevent
cytokine synthesis
by immune cells, such as T cells, and thus acts as an immunosuppressant.
I~Ioreover, a lack
of costimulation may also be sufficient to energize the T cells, thereby
inducing tolerance in
a subject. Induction of long-term tolerance by B lymphocyte antigen-blocking
reagents may
avoid the necessity of repeated administration of these blocking reagents. To
achieve
sufficient immunosuppression or tolerance in a subject, it may also be
necessary to block the
function of a combination of B ly~nphocyte antigens.
The efficacy of particular therapeutic compositions in preventing organ
transplant
rejection or GVHD can be assessed using animal models that are predictive of
efficacy in
humans. Examples of appropriate systems which can be used include allogeneic
cardiac
grafts in rats and xenogeneic pancreatic islet cell grafts in mice, both of
which have been
used to examine the immunosuppressive effects of CTLA4Ig fusion proteins in
vivo as
described in Lenschow et al., Science 257:789-792 (1992) and Turka et al.,
Proc. Natl. Aced.
Sci LTSA, 89:11102-11105 (1992). In addition, murine models of GVHD (see Paul
ed.,
Fundamental Immunology, Raven Press, New York, 1989, pp. 846-847) can be used
to
determine the effect of therapeutic compositions of the invention on the
development of that
disease.
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Blocking antigen function may also be therapeutically useful for treating
autoimmune diseases. Many autoimmune disorders are the result of inappropriate
activation
of T cells that are reactive against self tissue and which promote the
production of cytokines
and autoantibodies involved in the pathology of the diseases. Preventing the
activation of
5 autoreactive T cells may reduce or eliminate disease symptoms.
Administration of reagents
which block stimulation of T cells can be used to inhibit T cell activation
and prevent
production of autoantibodies or T cell-derived cytokines which may be involved
in the
disease process. Additionally, blocking reagents may induce antigen-specific
tolerance of
autoreactive T cells which could lead to long-term relief from the disease.
The efficacy of
10 blocking reagents in preventing or alleviating autoimmune disorders can be
determined
using a number of well-characterized animal models of human autoimmune
diseases.
Examples include murine experimental autoimmune encephalitis, systemic lupus
erythmatosis in MRL/lpr/lpr mice or NZB hybrid mice, murine autoimmune
collagen
arthritis, diabetes mellitus in NOD mice and BB rats, and murine experimental
myasthenia
15 gravis (see Paul ed., Fundamental Immunology, Raven Press, New York, 199,
pp.
X40-856).
LTpregulation of an antigen function (e.g., a B lymphocyte antigen function),
as a
means of up regulating immune responses, may also be useful in therapy.
Upregulation of
immune responses may be in the form of enhancing an existing immune response
or eliciting
20 an initial immune response. For example, enhancing an immune response may
be useful in
cases of viral infection, including systemic viral diseases such as influenza,
the coanmon
cold, and encephalitis.
Alternatively, anti-viral immune responses may be enhanced in an infected
patient by
removing T cells from the patient, costimulating the T cells in vitro with
viral antigen-pulsed
25 APCs either expressing a peptide of the present invention or together with
a stimulatory
form of a soluble peptide of the present invention and reintroducing the in
vitro activated T
cells into the patient. Another method of enhancing anti-viral immune
responses would be to
isolate infected cells from a patient, transfect them with a nucleic acid
encoding a protein of
the present invention as described herein such that the cells express all or a
portion of the
30 protein on their surface, and reintroduce the transfected cells into the
patient. The infected
cells would now be capable of delivering a costimulatory signal to, and
thereby activate, T
cells in vivo.
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56
A polypeptide of the present invention may provide the necessary stimulation
signal
to T cells to induce a T cell mediated immune response against the transfected
tumor cells.
In addition, tumor cells which lack MHC class I or MHC class II molecules, or
which fail to
reexpress sufficient mounts of MHC class I or MHC class II molecules, can be
transfected
with nucleic acid encoding all or a portion of (e.g., a cytoplasmic-domain
truncated portion)
of an MHC class I alpha chain protein and (32 microglobulin protein or an MHC
class II
alpha chain protein and an MHC class II beta chain protein to thereby express
MHC class I
or MHC class II proteins on the cell surface. Expression of the appropriate
class I or class II
MHC in conjunction with a peptide having the activity of a B lymphocyte
antigen (e.g.,
B7-1, B7-2, B7-3) induces a T cell mediated immune response against the
transfected tumor
cell. Optionally, a gene encoding an antisense construct which blocks
expression of an MHC
class II associated protein, such as the invariant chain, can also be
cotransfected with a I~NA
encoding a peptide having the activity of a B lymphocyte antigen to promote
presentation of
tumor associated antigens and induce tumor specific immunity. Thus, the
induction of a T
cell mediated immune response in a human subject may be sufficient to overcome
tumor-specific tolerance in the subject.
The activity of a protein of the invention may, among other means, be measured
by
the following methods:
Suitable assays for thymocyte or splenocyte cytotoxicity include, without
limitation,
those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A.
M. I~ruisbeek,
I~. H. Margulies, E. M. Shevach, ~. Strober, Pub. C'areene Publishing
Associates and
Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function
3.1-3.19;
Chapter 7, Immunologic studies in Humans); Herrmann et al., Proc. Natl. Acad.
Sci. USA
78:2488-2492, 1981; Herrmann et al., J. Immunol. 128:1968-1974, 1982; Handa et
al., J.
Immunol. 135:1564-1572, 1985; Takai et al., I. Immunol. 137:3494-3500, 1986;
Takai et al.,
J. Immunol. 140:508-512, 1988; Bowman et al., J. Virology 61:1992-1998;
Bertagnolli et
al., Cellular Immunology 133:327-341, 1991; Brown et al., J. Immunol. 153:3079-
3092,
1994.
Assays for T-cell-dependent immunoglobulin responses and isotype switching
(which will identify, among others, proteins that modulate T-cell dependent
antibody
responses and that affect Thl/Th2 profiles) include, without limitation, those
described in:
Maliszewski, J. Immunol. 144:3028-3033, 1990; and Assays for B cell function:
In vitro
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57
antibody production, Mond, J. J. and Brunswick, M. In Current Protocols in
Immunology. J.
E. e.a. Coligan eds. Vol 1 pp. 3.8.1-3.8.16, John Wiley and Sons, Toronto.
1994.
Mixed lymphocyte reaction (MLR) assays (which will identify, among others,
proteins that generate predominantly Thl and CTL responses) include, without
limitation,
those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A.
M. Kruisbeek,
D. H. Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates
and
Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function
3.1-3.19;
Chapter 7, Immunologic studies in Humans); Takai et al., J. Immunol. 137:3494-
3500, 1986;
Takai et al., J. Immunol. 140:508-512, 1988; Bertagnolli et al., J. Immunol.
149:3778-3783,
1992.
Dendritic cell-dependent assays (which will identify, among others, proteins
expressed by dendritic cells that activate naive T-cells) include, without
limitation, those
described in: Guery et al., J. Immunol. 134:536-544, 1995; Inaba et al.,
Journal of
Experimental Medicine 173:549-559, 1991; Macatonia et al., Journal of
Immunology
154:5071-5079, 1995; Porgador et al., Journal of Experimental Medicine 182:255-
260,
1995; Nair et al., Journal of Virology 67:4062-4069, 1993; Huang et al.,
Science
264:961-965, 1994; Macatonia et al., Journal of Experimental Medicine 169:1255-
1264,
1989; Bhardwaj et al., Journal of Clinical Investigation 94:797-807, 1994; and
Inaba et al.,
Journal of Experimental Medicine 172:631-640, 1990.
Assays for lymphocyte survival/apoptosis (which will identify, among others,
proteins that prevent apoptosis after superantigen induction and proteins that
regulate
lymphocyte homeostasis) include, without limitation, those described in: Dart'
lciewic~ et
al., Cytometry 13:795-808, 1992; Gorczyca et al., Leukemia 7:659-670, 1993;
Gorczyca et
al., Cancer Research 53:1945-1951, 1993; Itoh et al., Cell 66:233-243, 1991;
Zacharchuk,
Journal of Immunology 145:4037-4045, 1990; Zamai et al., Cytometry 14:891-897,
1993;
Gorczyca et al., International Journal of ~ncology 1:639-648, 1992.
Assays for proteins that influence early steps of T-cell commitment and
development
include, without limitation, those described in: Antica et al., Blood 84:111-
117, 1994; Fine
et al., Cellular Immunology 155:111-122, 1994; Galy et al., Blood 85:2770-
2778, 1995;
Toki et al., Proc. Nat. Acad Sci. USA 88:7548-7551, 1991.
4.10.8 ACTIVIN/INHIBIN ACTIVITY
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58
A polypeptide of the present invention may also exhibit activin- or inhibin-
related
activities. A polynucleotide of the invention may encode a polypeptide
exhibiting such
characteristics. Inhibins are characterized by their ability to inhibit the
release of follicle
stimulating hormone (FSH), while activins and are characterized by their
ability to stimulate
the release of follicle stimulating hormone (FSH). Thus, a polypeptide of the
present
invention, alone or in heterodimers with a member of the inhibin family, may
be useful as a
contraceptive based on the ability of inhibins to decrease fertility in female
mammals and
decrease spermatogenesis in male mammals. Administration of sufficient amounts
of other
inhibins can induce infertility in these mammals. Alternatively, the
polypeptide of the
invention, as a homodimer or as a heterodimer with other protein subunits of
the inhibin
group, may be useful as a fertility inducing therapeutic, based upon the
ability of activin
molecules in stimulating FSH release from cells of the anterior pituitary.
See, for example,
U.S. Pat. No. 4,798,885. A polypeptide of the invention may also be useful for
advancement
of the onset of fertility in sexually immature mammals, so as to increase the
lifetime
reproductive performance of domestic animals such as, but not limited to,
cows, sheep and
pigs.
The activity of a polypeptide of the invention may, among other means, be
measured
by the following methods.
Assays for activin/inhibin activity include, without limitation, those
described in:
Vale et al., Endocrinology 91:562-572, 1972; Ling et al., Nature 321:779-782,
1986; Vale et
al., Nature 321:776-779, 1986; I~JLason et al., Nature 318:659-663, 1955;
Forage et al., Pros.
Natl. Acad. Sci. USA 83:3091-3095, 1986.
4.10.9 CHEMOTACTIC/CHEM~KINETIC ACTIVITY
A polypeptide of the present invention may be involved in chemotactic or
chemokinetic activity for mammalian cells, including, for example, monocytes,
fibroblasts,
neutrophils, T-cells, mast cells, eosinophils, epithelial and/or endothelial
cells. A
polynucleotide of the invention can encode a polypeptide exhibiting such
attributes.
Chemotactic and chemokinetic receptor activation can be used to mobilize or
attract a
desired cell population to a desired site of action. Chemotactic or
chemokinetic compositions
(e.g. proteins, antibodies, binding partners, or modulators of the invention)
provide particular
advantages in treatment of wounds and other trauma to tissues, as well as in
treatment of
localized infections. For example, attraction of lymphocytes, monocytes or
neutrophils to
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59
tumors or sites of infection may result in improved immune responses against
the tumor or
infecting agent.
A protein or peptide has chemotactic activity for a particular cell population
if it can
stimulate, directly or indirectly, the directed orientation or movement of
such cell
population. Preferably, the protein or peptide has the ability to directly
stimulate directed
movement of cells. Whether a particular protein has chemotactic activity for a
population of
cells can be readily determined by employing such protein or peptide in any
known assay for
cell chemotaxis.
Therapeutic compositions of the invention can be used in the following:
Assays for chemotactic activity (which will identify proteins that induce or
prevent
chemotaxis) consist of assays that measure the ability of a protein to induce
the migration of
cells across a membrane as well as the ability of a protein to induce the
adhesion of one cell
population to another cell population. Suitable assays for movement and
adhesion include,
without limitation, those described in: Current Protocols in Immunology, Ed by
J. E.
Coligan, A. M. I~ruisbeek, D. H. Marguiles, E. M. Shevach, W. Strober, Pub.
Greene
Publishing Associates and Wiley-Interscience (Chapter 6.12, Measurement of
alpha and beta
Chemokines 6.12.1-6.12.28; Taub et al. J. Clin. Invest. 95:1370-1376, 1995;
Lind et al.
APMIS 103:140-146, 1995; Muller et al Eur. J. Immunol. 25:1744-1748; Gruber et
al. J. of
Immunol. 152:5860-5867, 1994; Johnston et al. J. of Immunol. 153:1762-1768,
1994.
4.10.10 ~TlEl~I~~~I°AT1~C AI's ~CH~~i~L~~"1~ AC'Tl~flT~
A polypeptide of the invention may also be involved in hemostatis or
thrombolysis or
thrombosis. A polynucleotide of the invention can encode a polypeptide
exhibiting such
attributes. Compositions may be useful in treatment of various coagulation
disorders
(including hereditary disorders, such as hemophiliac) or to enhance
coagulation and other
hemostatic events in treating wounds resulting from trauma, surgery or other
causes. A
composition of the invention may also be useful for dissolving or inhibiting
formation of
thromboses and for treatment and prevention of conditions resulting therefrom
(such as, for
example, infarction of cardiac and central nervous system vessels (e.g.,
stroke).
Therapeutic compositions of the invention can be used in the following:
Assay for hemostatic and thrombolytic activity include, without limitation,
those
described in: Linet et al., J. Clin. Pharmacol. 26:131-140, 1986; Burdick et
al., Thrombosis
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Res. 45:413-419, 1987; Humphrey et al., Fibrinolysis 5:71-79 (1991); Schaub,
Prostaglandins 35:467-474, 1988.
4.10.11 CANCER DIAGNOSIS AND THERAPY
5 Polypeptides of the invention may be involved in cancer cell generation,
proliferation
or metastasis. Detection of the presence or amount of polynucleotides or
polypeptides of the
invention may be useful for the diagnosis and/or prognosis of one or more
types of cancer.
For example, the presence or increased expression of a
polynucleotide/polypeptide of the
invention may indicate a hereditary risk of cancer, a precancerous condition,
or an ongoing
10 malignancy. Conversely, a defect in the gene or absence of the polypeptide
may be
associated with a cancer condition. Identification of single nucleotide
polymorphisms
associated with cancer or a predisposition to cancer may also be useful for
diagnosis or
prognosis.
Cancer treatments promote tumor regression by inhibiting tumor cell
proliferation,
15 inhibiting angiogenesis (growth of new blood vessels that is necessary to
support tumor
growth) and/or prohibiting metastasis by reducing tumor cell motility or
invasiveness.
Therapeutic compositions of the inveaxtion may be effective in adult and
pediatric oncology
including in solid phase tumors/malignancies, locally advanced tumors, human
soft tissue
sarcomas, metastatic cancer, including lymphatic metastases, blood cell
malignancies
20 including multiple myeloma, acute and chronic leukemias, and lymphomas,
head and neck
cancers including mouth cancer, larynx can cer and thyroid cancer, lung
cancers including
small cell carcinoma and non-Snlall cell cancers, breast cancers including
small cell
carcinoma and ductal carcinoma, gastrointestinal cancers including esophageal
cancer,
stomach cancer, colon cancer, colorectal cancer and polyps associated with
colorectal
25 neoplasia, pancreatic cancers, liver cancer, urologic cancers including
bladder cancer and
prostate cancer, malignancies of the female genital tract including ovarian
carcinoma, uterine
(including endometrial) cancers, and solid tumor in the ovarian follicle,
kidney cancers
including renal cell carcinoma, brain cancers including intrinsic brain
tumors,
neuroblastoma, astrocytic brain tumors, gliomas, metastatic tumor cell
invasion in the central
30 nervous system, bone cancers including osteomas, skin cancers including
malignant
melanoma, tumor progression of human skin keratinocytes, squamous cell
carcinoma, basal
cell carcinoma, hemangiopericytoma and I~arposi's sarcoma.
Polypeptides, polynucleotides, or modulators of polypeptides of the invention
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61
(including inhibitors and stimulators of the biological activity of the
polypeptide of the
invention) may be administered to treat cancer. Therapeutic compositions can
be
administered in therapeutically effective dosages alone or in combination with
adjuvant
cancer therapy such as surgery, chemotherapy, radiotherapy, thermotherapy, and
laser
therapy, and may provide a beneficial effect, e.g. reducing tumor size,
slowing rate of tumor
growth, inhibiting metastasis, or otherwise improving overall clinical
condition, without
necessarily eradicating the cancer.
The composition can also be administered in therapeutically effective amounts
as a
portion of an anti-cancer cocktail. An anti-cancer cocktail is a mixture of
the polypeptide or
modulator of the invention with one or more anti-cancer drugs in addition to a
pharnlaceutically acceptable carrier for delivery. The use of anti-cancer
cocktails as a cancer
treatment is routine. Anti-cancer drugs that are well known in the art and can
be used as a
treatment in combination with the polypeptide or modulator of the invention
include:
Actinomycin D, Aminoglutethimide, Asparaginase, Bleomycin, Busulfan,
Carboplatin,
Carmustine, Chlorambucil, Cisplatin (cis-DDP), Cyclophosphamide, Cytarabine
HCl
(Cytosine arabinoside), Dacarbazine, Dactinomycin, Daun~rubicin HCI,
Doxorubicin HCI,
Estramustine phosphate sodium, Etoposide (V16-213), Floxuridine, 5-
Fluorouracil (5-Fu),
Flutamide, Hydroxyurea (hydroxycarbamide), Ifosfamide, Interferon Alpha-2a,
Interferon
Alpha-2,b, Leuprolide acetate (LHRH-releasing factor analog), Lomustine,
Mechlorethamine
HCl (nitrogen mustard), Melphalan, Mercaptopurine, Mesna, Methotrexate (MTX),
Mitomycin, Mitoxantrone HCI, ~ctreotide, Plicamycin, Procarbazine HCI,
Streptozocin,
Tamoxifen citrate, Thioguanine, Thi~tepa, Vinblastine sulfate, Vincristine
sulfate,
Amsacrine, Azacitidine, Hexamethylmelamine, Interleukin-2, Mitoguazone,
Pentostatin,
Semustine, Teniposide, and Vindesine sulfate.
In addition, therapeutic compositions of the invention may be used for
prophylactic
treatment of cancer. There are hereditary conditions and/or environmental
situations (e.g.
exposure to carcinogens) known in the art that predispose an individual to
developing
cancers. Under these circumstances, it may be beneficial to treat these
individuals with
therapeutically effective doses of the polypeptide of the invention to reduce
the risk of
developing cancers.
In vitro models can be used to determine the effective doses of the
polypeptide of the
invention as a potential cancer treatment. These ira vitro models include
proliferation assays
of cultured tumor cells, growth of cultured tumor cells in soft agar (see
Freshney, (1987)
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62
Culture of Animal Cells: A Manual of Basic Technique, Wily-Liss, New York, NY
Ch 18
and Ch 21), tumor systems in nude mice as described in Giovanella et al., J.
Natl. Can. Inst.,
52: 921-30 (1974), mobility and invasive potential of tumor cells in Boyden
Chamber assays
as described in Pilkington et al., Anticancer Res., 17: 4107-9 (1997), and
angiogenesis
assays such as induction of vascularization of the chick chorioallantoic
membrane or
induction of vascular endothelial cell migration as described in Ribatta et
al., Intl. J. Dev.
Biol., 40: 1189-97 (1999) and Li et al., Clin. Exp. Metastasis, 17:423-9
(1999), respectively.
Suitable tumor cells lines are available, e.g. from American Type Tissue
Culture Collection
catalogs.
4.10.12 RECEPTOR/LIGAND ACTIVITY
A polypeptide of the present invention may also demonstrate activity as
receptor,
receptor ligand or inhibitor or agonist of receptor/ligand interactions. A
polynucleotide of
the invention can encode a polypeptide exhibiting such characteristics.
Examples of such
receptors and ligands include, without limitation, cytokine receptors and
their ligands,
receptor kinases and their ligands, receptor phosphatases and their ligands,
receptors
involved in cell-cell interactions and their ligands (including without
limitation, cellular
adhesion molecules (such as selectins, integrins and their ligands) and
recept~r/ligand pairs
involved in antigen presentation, antigen recognition and development of
cellular and
humoral immune responses. Receptors and ligands are also useful for screening
of potential
peptide ~r small molecule inhibitors of the relevant receptor/ligand
interaction. A protein of
the present invention (including, without limitation, fragments of receptors
and ligands) may
themselves be useful as inhibitors of receptor/ligand interactions.
'The activity of a polypeptide of the invention may, among other means, be
measured
by the following methods:
Suitable assays for receptor-ligand activity include without limitation those
described
in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. I~ruisbeek, D.
H.
Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and
Wiley-
Interscience (Chapter 7.28, Measurement of Cellular Adhesion under static
conditions
7.28.1- 7.28.22), Takai et al., Proc. Natl. Acad. Sci. LTSA 84:6864-6868,
1987; Bierer et al.,
J. Exp. Med. 168:1145-1156, 1988; Rosenstein et al., J. Exp. Med. 169:149-160
1989;
Stoltenborg et al., J. Immunol. Methods 175:59-68, 1994; Stitt et al., Cell
80:661-670, 1995.
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63
By way of example, the polypeptides of the invention may be used as a receptor
for a
ligand(s) thereby transmitting the biological activity of that ligand(s).
Ligands may be
identified through binding assays, affinity chromatography, dihybrid screening
assays,
BIAcore assays, gel overlay assays, or other methods known in the art.
Studies characterizing drugs or proteins as agonist or antagonist or partial
agonists or
a partial antagonist require the use of other proteins as competing ligands.
The polypeptides
of the present invention or ligand(s) thereof may be labeled by being coupled
to
radioisotopes, colorimetric molecules or a toxin molecules by conventional
methods.
("Guide to Protein Purification" Murray P. Deutscher (ed) Methods in
Enzymology Vol. 182
(1990) Academic Press, Inc. San Diego). Examples of radioisotopes include, but
are not
limited to, tritium and carbon-14 . Examples of colorimetric molecules
include, but are not
limited to, fluorescent molecules such as fluorescamine, or rhodamine or other
colorimetric
molecules. Examples of toxins include, but are not limited, to ricin.
4.10.13 DRUG SCREENING
This invention is particularly useful for screening chemical compounds by
using the
novel polypeptides ~r binding fragments thereof in any of a variety of drug
screening
techniques. The polypeptides or fragments employed in such a test may either
be flee in
solution, affixed to a solid support, borne on a cell surface or located
intracellularly. One
method of drug screening utilizes eukaryotic or prokaryotic host cells which
are stably
transformed v~ith recombinant amcleic acids e~epressing the polypeptidc or a
fragment
thereof. Drugs are screened against such transformed cells in competitive
binding assays.
Such cells, either in viable or fixed form, can be used for standard binding
assays. ~ne may
measure, for example, the formation of complexes between polypeptides of the
invention or
fiagments and the agent being tested or examine the diminution in complex
forniation
between the novel polypeptides and an appropriate cell line, which are well
known in the art.
Sources for test compounds that may be screened for ability to bind to or
modulate
(i.e., increase or decrease) the activity of polypeptides of the invention
include (1) inorganic
and organic chemical libraries, (2) natural product libraries, and (3)
combinatorial libraries
comprised of either random or mimetic peptides, oligonucleotides or organic
molecules.
Chemical libraries may be readily synthesized or purchased from a number of
commercial sources, and may include structural analogs of known compounds or
compounds
that are identified as "hits" or "leads" via natural product screening.
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64
The sources of natural product libraries are microorganisms (including
bacteria and
fungi), animals, plants or other vegetation, or marine organisms, and
libraries of mixtures for
screening may be created by: (1) fermentation and extraction of broths from
soil, plant or
marine microorganisms or (2) extraction of the organisms themselves. Natural
product
libraries include polyketides, non-ribosomal peptides, and (non-naturally
occurring) variants
thereof. For a review, see Sciezzce 282:63-68 (1998).
Combinatorial libraries are composed of large numbers of peptides,
oligonucleotides
or organic compounds and can be readily prepared by traditional automated
synthesis
methods, PCR, cloning or proprietary synthetic methods. Of particular interest
are peptide
and oligonucleotide combinatorial libraries. Still other libraries of interest
include peptide,
protein, peptidomimetic, multiparallel synthetic collection, recombinatorial,
and polypeptide
libraries. For a review of combinatorial chemistry and libraries created
therefrom, see
Myers, Gui~>~. Opirz. Biotechnol. 8:701-707 (1997). For reviews and examples
of
peptidomirnetic libraries, see Al-Obeidi et al., Mol. Biateclzzzol, 9(3):205-
23 (1998); Hruby
et al., C'uz~r O,nizz Cherrz Biol, 1(1):114-19 (1997); Dorner et al., Bio~Yg
Med Claezra,
4(5):709-15 (1996) (alkylated dipeptides).
Identification of modulators through use of the various libraries described
herein
permits modification of the candidate "hit" (or "lead") to optimize the
capacity of the "hit"
to bind a polypeptide of the invention. The molecules identified in the
binding assay are then
tested for antagonist or agonist activity in irz viv~ tissue culture or animal
models that are
well known in the art. In brief, the molecules are titrated into a plurality
of cell cultures or
animals and then tested for either cell/animal death or prolonged survival of
the animal/cells.
The binding molecules thus identified may be complexed with toxins, e.g.,
ricin or
cholera, or with other compounds that are toxic to cells such as
radioisotopes. 'The
toxin-binding molecule complex is then targeted to a tumor or other cell by
the specificity of
the binding molecule for a polypeptide of the invention. Alternatively, the
binding
molecules may be complexed with imaging agents for targeting and imaging
purposes.
4.10.14 ASSAY FOR RECEPTOR ACTIVITY
The invention also provides methods to detect specific binding of a
polypeptide e.g. a
ligand or a receptor. The art provides numerous assays particularly useful for
identifying
previously unknown binding partners for receptor polypeptides of the
invention. For
example, expression cloning using mammalian or bacterial cells, or dihybrid
screening
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assays can be used to identify polynucleotides encoding binding partners. As
another
example, affinity chromatography with the appropriate immobilized polypeptide
of the
invention can be used to isolate polypeptides that recognize and bind
polypeptides of the
invention. There are a number of different libraries used for the
identification of
5 compounds, and in particular small molecules, that modulate (i. e., increase
or decrease)
biological activity of a polypeptide of the invention. Ligands for receptor
polypeptides of the
invention can also be identified by adding exogenous ligands, or cocktails of
ligands to two
cells populations that are genetically identical except for the expression of
the receptor of the
invention: one cell population expresses the receptor of the invention whereas
the other does
10 not. The responses of the two cell populations to the addition of
ligands(s) are then
compared. Alternatively, an expression library can be co-expressed with the
polypeptide of
the invention in cells and assayed for an autocrine response to identify
potential ligand(s). As
still another example, BIAcore assays, gel overlay assays, or other methods
known in the art
can be used to identify binding partner polypeptides, including, (1) organic
and inorganic
15 chemical libraries, (2) natural product libraries, and (3) combinatorial
libraries comprised of
random peptides, oligonucleotides or organic molecules.
The role of downstream intracellular signaling molecules in the signaling
cascade of
the polypeptide of the invention can be deternzined. For example, a chimeric
protein in
which the cytoplasmic domain of the polypeptide of the invention is fused to
the
20 extracellular portion of a protein, whose ligand has been identified, is
produced in a host
cell. 'The cell is then incubated with the ligand specific for the
extracellular portion of the
chimeric protein, thereby activating the chimeric receptor. Known downstream
proteins
involved in intracellular signaling can then be assayed for expected
modifications i.e.
phosphorylation. ~ther methods known to those in the art can also be used to
identify
25 signaling molecules involved in receptor activity.
4.10.15 ANTI-INFLAMMATOlIY ACTIVITY
Compositions of the present invention may also exhibit anti-inflammatory
activity.
The anti-inflammatory activity may be achieved by providing a stimulus to
cells involved in
30 the inflammatory response, by inhibiting or promoting cell-cell
interactions (such as, for
example, cell adhesion), by inhibiting or promoting chemotaxis of cells
involved in the
inflammatory process, inhibiting or promoting cell extravasation, or by
stimulating or
suppressing production of other factors which more directly inhibit or promote
an
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66
inflammatory response. Compositions with such activities can be used to treat
inflammatory
conditions including chronic or acute conditions), including without
limitation intimation
associated with infection (such as septic shock, sepsis or systemic
inflammatory response
syndrome (SIRS)), ischemia-reperfusion injury, endotoxin lethality, arthritis,
complement-mediated hyperacute rejection, nephritis, cytokine or chemokine-
induced lung
injury, inflammatory bowel disease, Crohn's disease or resulting from over
production of
cytokines such as TNF or IL-1. Compositions of the invention may also be
useful to treat
anaphylaxis and hypersensitivity to an antigenic substance or material.
Compositions of this
invention may be utilized to prevent or treat conditions such as, but not
limited to, sepsis,
acute pancreatitis, endotoxin shock, cytokine induced shock, rheumatoid
arthritis, chronic
inflammatory arthritis, pancreatic cell damage from diabetes mellitus type 1,
graft versus
host disease, inflanunatory bowel disease, inflamation associated with
pulmonary disease,
other autoimmune disease or inflammatory disease, an antiproliferative agent
such as for
acute or chronic mylegenous leukemia or in the prevention of premature labor
secondary to
intrauterine infections.
4.10.16 LEUI~MI~S
Leukemias and related disorders may be treated or prevented by administration
of a
therapeutic that promotes or inhibits function of the polynucleotides and/or
polypeptides of
the invention. Such leukemias and related disorders include but are not
limited to acute
leukemia, acute lymphocytic leukemia, acute myelocytic leukemia, myeloblastic,
promyelocytic, myelomonocytic, monocytic, erythroleukemia, chronic leukemia,
chronic
myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia (for a
review of such
disorders, see Fishman et al., 195, Medicine, 2,d Ed., J.B. Lippincott Co.,
Philadelphia).
4.10.17 NERVOUS SYSTEM DISORDERS
Nervous system disorders, involving cell types which can be tested for
efficacy of
intervention with compounds that modulate the activity of the polynucleotides
and/or
polypeptides of the invention, and which can be treated upon thus observing an
indication of
therapeutic utility, include but are not limited to nervous system injuries,
and diseases or
disorders which result in either a disconnection of axons, a diminution or
degeneration of
neurons, or demyelination. Nervous system lesions which may be treated in a
patient
(including human and non-human mammalian patients) according to the invention
include
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but are not limited to the following lesions of either the central (including
spinal cord, brain)
or peripheral nervous systems:
(i) traumatic lesions, including lesions caused by physical injury or
associated
with surgery, for example, lesions which sever a portion of the nervous
system, or
compression injuries;
(ii) ischemic lesions, in which a lack of oxygen in a portion of the nervous
system
results in neuronal injury or death, including cerebral infarction or
ischemia, or spinal cord
infarction or ischemia;
(iii) infectious lesions, in which a portion of the nervous system is
destroyed or
injured as a result of infection, for example, by an abscess or associated
with infection by
human immunodericiency virus, herpes zoster, or herpes simplex virus or with
Lyme
disease, tuberculosis, syphilis;
(iv) degenerative lesions, in which a portion of the nervous system is
destroyed or
injured as a result of a degenerative process including but not limited to
degeneration
associated with Parkins~n's disease, Alzheimer's disease, Huntington's chorea,
or
amyotrophic lateral sclerosis;
(v) lesions associated with nutritional diseases or disorders, in which a
portion ~f
the nervous system is destroyed or injured by a nutritional disorder or
dis~rder ~f
metabolism including but not limited to, vitamin B 12 deficiency, folic acid
deficiency,
Wernicke disease, tobacco-alcohol amblyopia, Marchiafava-Bignami disease
(primary
degeneration of the c~rpus callesum), and alcoholic cerebellar degeneration;
(vi) neurological lesions associated with systemic diseases including but not
limited to diabetes (diabetic neur~pathy, Bell's palsy), systemic lupus
erythematosus,
carcinoma, or sarcoidosis;
(vii) lesions caused by toxic substances including alcohol, lead, or
particular
neurotoxins; and
(viii) demyelinated lesions in which a portion of the nervous system is
destroyed or
injured by a demyelinating disease including but not limited to multiple
sclerosis, human
immunodeficiency virus-associated myelopathy, transverse myelopathy or various
etiologies, progressive multifocal leukoencephalopathy, and central pontine
myelinolysis.
Therapeutics which are useful according to the invention for treatment of a
nervous
system disorder may be selected by testing for biological activity in
promoting the survival
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68
or differentiation of neurons. For example, and not by way of limitation,
therapeutics which
elicit any of the following effects may be useful according to the invention:
(i) increased survival time of neurons in culture;
(ii) increased sprouting of neurons in culture or in vivo;
(iii) increased production of a neuron-associated molecule in culture or in
vivo,
e.g., choline acetyltransferase or acetylcholinesterase with respect to motor
neurons; or
(iv) decreased symptoms of neuron dysfunction in vivo.
Such effects may be measured by any method known in the art. In preferred,
non-limiting embodiments, increased survival of neurons may be measured by the
method
set forth in Arakawa et al. (1990, J. Neurosci. 10:3507-3515); increased
sprouting of neurons
may be detected by methods set forth in Pestronk et al. (1980, Exp. Neurol.
70:65-82) or
Brown et al. (1981, Ann. Rev. Neurosci. 4:17-42); increased production of
neuron-associated molecules may be measured by bioassay, enzymatic assay,
antibody
binding, Northern blot assay, etc., depending on the molecule to be measured;
and motor
neuron dysfunction may be measured by assessing the physical manifestation of
motor
neuron disorder, e.g., weakness, motor neuron conduction velocity, or
functional disability.
In speciEc embodiments, motor neuron disorders that may be treated according
to the
invention include but are not limited to disorders such as infarction,
infection, exp~sure to
toxin, trauma, surgical damage, degenerative disease or malignancy that may
affect motor
neurons as well as other components of the nervous system, as well as
disorders that
selectively affect neurons such as amyotrophic lateral sclerosis, and
including but not limited
to progressive spinal muscular atrophy, progressive bulbar palsy, primary
lateral sclerosis,
infantile and juvenile muscular atrophy, progressive bulbar paralysis of
childhood (Fazio-
Londe syndrome), poliomyelitis and the post polio syndrome, and Hereditary
Motorsensory
Neuropathy (Charcot-Marie-Tooth Disease).
4.10.18 OTHER ACTIVITIES
A polypeptide of the invention may also exhibit one or more of the following
additional activities or effects: inhibiting the growth, infection or function
of, or killing,
infectious agents, including, without limitation, bacteria, viruses, fungi and
other parasites;
effecting (suppressing or eiW ancing) bodily characteristics, including,
without limitation,
height, weight, hair color, eye color, skin, fat to lean ratio or other tissue
pigmentation, or
organ or body part size or shape (such as, for example, breast augmentation or
diminution,
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change in bone form or shape); effecting biorhythms or circadian cycles or
rhythms;
effecting the fertility of male or female subjects; effecting the metabolism,
catabolism,
anabolism, processing, utilization, storage or elimination of dietary fat,
lipid, protein,
carbohydrate, vitamins, minerals, co-factors or other nutritional factors or
component(s);
effecting behavioral characteristics, including, without limitation, appetite,
libido, stress,
cognition (including cognitive disorders), depression (including depressive
disorders) and
violent behaviors; providing analgesic effects or other pain reducing effects;
promoting
differentiation and growth of embryonic stem cells in lineages other than
hematopoietic
lineages; hormonal or endocrine activity; in the case of enzymes, correcting
deficiencies of
the enzyme and treating deficiency-related diseases; treatment of
hyperproliferative
disorders (such as, for example, psoriasis); immunoglobulin-like activity
(such as, for
example, the ability to bind antigens or complement); and the ability to act
as an antigen in a
vaccine composition to raise an immune response against such protein or
another material or
entity which is cross-reactive with such protein.
4.10.19 I7IZi;T~TTIFICA'I°I~T'~ ~F P~LI~RPI~IST~I~
T'he demonstration of polymorphisms makes possible the identification of such
polymorphisms in human subjects and the pharmacogenetic use of this
information for
diagnosis and treatment. Such polymorphisms may be associated with, e.g.,
differential
predisposition or susceptibility to various disease states (such as disorders
involving
inflammation or nnmune response) or a differential response to drdbg
administration, and this
genetic information can be used to tailor preventive or therapeutic treatment
appropriately.
For example, the existence of a polymorphism associated with a predisposition
to
inflammation or autoimmune disease makes possible the diagnosis of this
condition in
humans by identifying the presence of the polymorphism.
Polymorphisms can be identified in a variety of ways known in the art which
all
generally involve obtaining a sample from a patient, analyzing DNA from the
sample,
optionally involving isolation or amplification of the DNA, and identifying
the presence of
the polymorphism in the DNA. For example, PCR may be used to amplify an
appropriate
fragment of genomic DNA which may then be sequenced. Alternatively, the DNA
may be
subjected to allele-specific oligonucleotide hybridization (in which
appropriate
oligonucleotides are hybridized to the DNA under conditions permitting
detection of a single
base mismatch) or to a single nucleotide extension assay (in which an
oligonucleotide that
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hybridizes immediately adjacent to the position of the polymorphism is
extended with one or
more labeled nucleotides). In addition, traditional restriction fragment
length polymorphism
analysis (using restriction enzymes that provide differential digestion of the
genomic DNA
depending on the presence or absence of the polymorphism) may be performed.
Arrays with
nucleotide sequences of the present invention can be used to detect
polymorphisms. The
array can comprise modified nucleotide sequences of the present invention in
order to detect
the nucleotide sequences of the present invention. In the alternative, any one
of the
nucleotide sequences of the present invention can be placed on the array to
detect changes
from those sequences.
10 Alternatively a polymorphism resulting in a change in the amino acid
sequence could
also be detected by detecting a corresponding change in amino acid sequence of
the protein,
e.g., by an antibody specific to the variant sequence.
4.10.20 ARTHRITIS AND INFLAMMATION
15 The immunosuppressive effects of the compositions of the invention against
rheumatoid arthritis is determined in an experimental animal model system. The
experimental model system is adjuvant induced arthritis in rats, and the
protocol is described
by J. Holoshitz, et at., 1983, Science, 219:56, or by 13. V6~aksman et al.,
1963, Int. Arch.
Allergy Appl. Immunol., 23:129. Induction of the disease can be caused by a
single
20 injection, generally intradermally, of a suspension of killed Mycobacterium
tuberculosis in
complete Freund's adjuvant (CFA). T'he route of injection can vary, but rats
may be injected
at the base of the tail with an adjuvant mixture. T'he polypeptide is
administered in phosphate
buffered solution (PBS) at a dose of about 1-5 mg/kg. The control consists of
administering
PBS only.
25 The procedure for testing the effects of the test compound would consist of
intradermally injecting killed Mycobacterium tuberculosis in CFA followed by
immediately
administering the test compound and subsequent treatment every other day until
day 24. At
14, 15, 18, 20, 22, and 24 days after injection of Mycobacterium CFA, an
overall arthritis
score may be obtained as described by J. Holoskitz above. An analysis of the
data would
30 reveal that the test compound would have a dramatic affect on the swelling
of the joints as
measured by a decrease of the arthritis score.
4.11 THERAPEUTIC METHODS
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The compositions (including polypeptide fragments, analogs, variants and
antibodies
or other binding partners or modulators including antisense polynucleotides)
of the invention
have numerous applications in a variety of therapeutic methods. Examples of
therapeutic
applications include, but are not limited to, those exemplified herein.
4.11.1 EXAMPLE
One embodiment of the invention is the administration of an effective amount
of the
polypeptides or other composition of the invention to individuals affected by
a disease or
disorder that can be modulated by regulating the peptides of the invention.
While the mode
of administration is not particularly important, parenteral administration is
preferred. An
exemplary mode of administration is to deliver an intravenous bolus. The
dosage of the
polypeptides or other composition of the invention will normally be determined
by the
prescribing physician. It is to be expected that the dosage will vary
according to the age,
weight, condition and response of the individual patient. Typically, the
amount of
polypeptide administered per dose will be in the range of about 0.01 pg/kg to
100 mg/kg of
body weight, with the preferred dose being about 0.1 ~glkg to 10 mg/kg of
patient body
weight. For parenteral administration, polypeptides of the invention will be
formulated in an
injectable fornz combined with a pharmaceutically acceptable parenteral
vehicle. Such
vehicles are well known in the art and examples include water, saline,
Ringer's solution,
dextrose solution, and solutions consisting of small amounts of the human
serum albumin.
The vehicle may contain minor amounts of additives that maintain the
isotonicity and
stability of the polypeptide or other active ingredient. The preparation of
such solutions is
within the skill of the art.
4.12 PHA CEUTICAL FORMULATIONS AND ROUTES OF
ADMINISTRATION
A protein or other composition of the present invention (from whatever source
derived, including without limitation from recombinant and non-recombinant
sources and
including antibodies and other binding partners of the polypeptides of the
invention) may be
administered to a patient in need, by itself, or in pharmaceutical
compositions where it is
mixed with suitable Garners or excipient(s) at doses to treat or ameliorate a
variety of
disorders. Such a composition may optionally contain (in addition to protein
or other active
ingredient and a carrier) diluents, fillers, salts, buffers, stabilizers,
solubilizers, and other
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72
materials well known in the art. The term "pharmaceutically acceptable" means
a non-toxic
material that does not interfere with the effectiveness of the biological
activity of the active
ingredient(s). The characteristics of the carrier will depend on the route of
administration.
The pharmaceutical composition of the invention may also contain cytokines,
lymphokines,
or other hematopoietic factors such as M-CSF, GM-CSF, TNF, IL-1, IL-2, IL-3,
IL-4, IL-5,
IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IFN, TNFO,
TNF1, TNF2,
G-CSF, Meg-CSF, thrombopoietin, stem cell factor, and erythropoietin. In
further
compositions, proteins of the invention may be combined with other agents
beneficial to the
treatment of the disease or disorder in question. These agents include various
growth factors
such as epidermal growth factor (EGF), platelet-derived growth factor (PDGF),
transforming
growth factors (TGF-a and TGF-(3), insulin-like growth factor (IGF)~ as well
as cytokines
described herein.
The pharmaceutical composition may further contain other agents which either
enhance the activity of the protein or other active ingredient or complement
its activity or
use in treatment. Such additional factors and/or agents may be included in the
pharmaceutical composition to produce a synergistic effect with protein or
other active
ingredient of the invention, or to minimize side effects. Conversely, protein
or other active
ingredient of the present invention may be included in formulations of the
particular clotting
factor, cytokine, lymphokine, other hematopoietic factor, thrombolytic or anti-
thrombotic
factor, or anti- inflammatory agent to minimize side effects of the clotting
factor, cytokine,
lyrnphokinc, other hernatopoietic factor, thrornbolytic or anti-thrornbotic
factor, or
anti-inflarnmat~ry agent (such as IL-lRa, IL-1 Hyl, IL-1 Hy2, anti-TNF,
c~rticoster~ids,
imrnunosuppressive agents). A protein ~f the present invention may be active
in multimers
(e.g., heterodimers or homodirners) or complexes with itself or other
proteins. As a result,
pharmaceutical compositions of the invention may comprise a protein ~f the
inventi~n in
such multimeric or complexed form.
As an alternative to being included in a pharmaceutical composition of the
invention
including a first protein, a second protein or a therapeutic agent may be
concurrently
administered with the first protein (e.g., at the same time, or at differing
times provided that
therapeutic concentrations of the combination of agents is achieved at the
treatment site).
Techniques for formulation and administration of the compounds of the instant
application
may be found in "Remington's Pharmaceutical Sciences," Mack Publishing Co.,
Easton, PA,
latest edition. A therapeutically effective dose further refers to that amount
of the compound
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73
sufficient to result in amelioration of symptoms, e.g., treatment, healing,
prevention or
amelioration of the relevant medical condition, or an increase in rate of
treatment, healing,
prevention or amelioration of such conditions. When applied to an individual
active
ingredient, administered alone, a therapeutically effective dose refers to
that ingredient
alone. When applied to a combination, a therapeutically effective dose refers
to combined
amounts of the active ingredients that result in the therapeutic effect,
whether administered
in combination, serially or simultaneously.
In practicing the method of treatment or use of the present invention, a
therapeutically effective amount of protein or other active ingredient of the
present invention
is administered to a mammal having a condition to be treated. Protein or other
active
ingredient of the present invention may be administered in accordance with the
method of
the invention either alone or in combination with other therapies such as
treatments
employing cytokines, lymphokines or other hematopoietic factors. When co-
administered
with one or more cytokines, lymphokines or other hematopoietic factors,
protein or other
active ingredient of the present invention may be administered either
simultaneously with
the cytokine(s), lymphokine(s), other hematopoietic factor(s), thrombolytic or
anti-thrombotic factors, or sequentially. If administered sequentially, the
attending physician
will decide on the appropriate sequence of administering protein or other
active ingredient of
the present invention in combination with cytokine(s), lymphokine(s), other
hematopoietic
factor(s), thrombolytic or anti-thrombotic factors.
~~.12.1 ~~~TLTT~~ ~1F A~T~I~~1I~~L°P~A'I"1~I~~T
Suitable routes of administration may, for example, include oral, rectal,
transmucosal, or intestinal administration; parenteral delivery, including
intramuscular,
subcutaneous, intramedullary injections, as well as intrathecal, direct
intraventricular,
intravenous, intraperitoneal, intranasal, or intraocular injections.
Administration of protein
or other active ingredient of the present invention used in the pharmaceutical
composition or
to practice the method of the present invention can be carried out in a
variety of conventional
ways, such as oral ingestion, inhalation, topical application or cutaneous,
subcutaneous,
intraperitoneal, parenteral or intravenous injection. Intravenous
administration to the patient
is preferred.
Alternately, one may administer the compound in a local rather than systemic
manner, for example, via injection of the compound directly into a arthritic
joints or in
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74
fibrotic tissue, often in a depot or sustained release formulation. In order
to prevent the
scarring process frequently occurnng as complication of glaucoma surgery, the
compounds
may be administered topically, for example, as eye drops. Furthermore, one may
administer
the drug in a targeted drug delivery system, for example, in a liposome coated
with a specific
antibody, targeting, for example, arthritic or fibrotic tissue. The liposomes
will be targeted
to and taken up selectively by the afflicted tissue.
The polypeptides of the invention are administered by any route that delivers
an
effective dosage to the desired site of action. The determination of a
suitable route of
administration and an effective dosage for a particular indication is within
the level of skill
in the art. Preferably for wound treatment, one administers the therapeutic
compound
directly to the site. Suitable dosage ranges for the polypeptides of the
invention can be
extrapolated from these dosages or from similar studies in appropriate animal
models.
Dosages can then be adjusted as necessary by the clinician to provide maximal
therapeutic
benefit.
4.12.2 C~I~SITI~I~dS/F~I~LU~.ATI~I~TS
Pharmaceutical compositions for use in accordance with the present invention
thus
may be formulated in a conventional manner using ~ne or more physiologically
acceptable
earners comprising excipients and auxiliaries which facilitate processing of
the active
compounds into preparations which can be used pharmaceutically. These
pharmaceutical
compositions may be manufactured in a manner that is itself known, ~e.~., by
means of
conventi~nal mixing, dissolving, granulating, dragee-making, levigating,
emulsifying,
encapsulating, entrapping or lyophilising processes. Proper formulation is
dependent upon
the route of administration ch~sen. When a therapeutically effective amount of
protein or
other active ingredient of the present invention is administered orally,
protein or other active
ingredient of the present invention will be in the form of a tablet, capsule,
powder, solution
or elixir. When administered in tablet form, the pharmaceutical composition of
the invention
may additionally contain a solid carrier such as a gelatin or an adjuvant. The
tablet, capsule,
and powder contain from about 5 to 95% protein or other active ingredient of
the present '
invention, and preferably from about 25 to 90% protein or other active
ingredient of the
present invention. When administered in liquid form, a liquid carrier such as
water,
petroleum, oils of animal or plant origin such as peanut oil, mineral oil,
soybean oil, or
sesame oil, or synthetic oils may be added. The liquid form of the
pharmaceutical
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composition may further contain physiological saline solution, dextrose or
other saccharide
solution, or glycols such as ethylene glycol, propylene glycol or polyethylene
glycol. When
administered in liquid form, the pharmaceutical composition contains from
about 0.5 to 90%
by weight of protein or other active ingredient of the present invention, and
preferably from
5 about 1 to 50% protein or other active ingredient of the present invention.
When a therapeutically effective amount of protein or other active ingredient
of the
present invention is administered by intravenous, cutaneous or
subcutaneous.injection,
protein or other active ingredient of the present invention will be in the
form of a
pyrogen-free, parenterally acceptable aqueous solution. The preparation of
such parenterally
10 acceptable protein or other active ingredient solutions, having due regard
to pH, isotonicity,
stability, and the like, is within the skill in the art. A preferred
pharmaceutical composition
for intravenous, cutaneous, or subcutaneous injection should contain, in
addition to protein
or other active ingredient of the present invention, an isotonic vehicle such
as Sodium
Chloride Injection, Ringer's Injection, Dextrose Injection, Dextrose and
Sodium Chloride
15 Injection, Lactated Ringer's Injection, or other vehicle as known in the
art. The
pharmaceutical composition of the present invention may also contain
stabilizers,
preservatives, buffers, antioxidants, or other additives known to those of
skill in the art. For
injection, the agents of the invention may be formulated in aqueous solutions,
preferably in
physiologically compatible buffers such as Hanks's solution, Ringer's
solution, or
20 physiological saline buffer. For transmucosal administration, penetrants
appropriate to the
barrier to be permeated are used in the formulation. Such penetrants are
generally known in
the art.
For oral administration, the compounds can be formulated readily by combining
the
active compounds with pharmaceutically acceptable carriers well known in the
art. Such
25 carriers enable the compounds of the invention to be formulated as tablets,
pills, dragees,
capsules, liquids, gels, syrups, slurnes, suspensions and the like, for oral
ingestion by a
patient to be treated. Pharmaceutical preparations for oral use can be
obtained from a solid
excipient, optionally grinding a resulting mixture, and processing the mixture
of granules,
after adding suitable auxiliaries, if desired, to obtain tablets or dragee
cores. Suitable
30 excipients are, in particular, fillers such as sugars, including lactose,
sucrose, mannitol, or
sorbitol; cellulose preparations such as, for example, maize starch, wheat
starch, rice starch,
potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-
cellulose,
sodium carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP). If desired,
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76
disintegrating agents may be added, such as the cross-linked polyvinyl
pyrrolidone, agar, or
alginic acid or a salt thereof such as sodium alginate. Dragee cores are
provided with
suitable coatings. For this purpose, concentrated sugar solutions may be used,
which may
optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel,
polyethylene glycol,
and/or titanium dioxide, lacquer solutions, and suitable organic solvents or
solvent mixtures.
Dyestuffs or pigments may be added to the tablets or dragee coatings for
identification or to
characterize different combinations of active compound doses.
Pharmaceutical preparations which can be used orally include push-fit capsules
made
of gelatin, as well as soft, sealed capsules made of gelatin and a
plasticizer, such as glycerol
or sorbitol. The push-fit capsules can contain the active ingredients in
admixture with filler
such as lactose, binders such as starches, and/or lubricants such as talc or
magnesium
stearate and, optionally, stabilizers. In soft capsules, the active compounds
may be dissolved
or suspended in suitable liquids, such as fatty oils, liquid paraffin, or
liquid polyethylene
glycols. In addition, stabilizers may be added. All formulations for oral
administration
should be in dosages suitable for such administration. For buccal
administration, the
compositions may take the form of tablets or lozenges formulated in
conventional manner.
For administration by inhalation, the compounds for use according to the
present
invention are conveniently delivered in the form of an aerosol spray
presentation from
pressurized packs or a nebuliser, with the use of a suitable propellant, e.g.,
dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane,
carbon dioxide
or other suitable gas. In the case of a pressurized aerosol the dosage unit
may be determined
by providing a valve to deliver a metered amount. Capsules and cartridges of,
e.g., gelatin
for use in an inhaler or insufflator may be formulated containing a powder mix
of the
compound and a suitable powder base such as lactose or starch. The compounds
may be
formulated for parenteral administration by injection, e.g., by bolus
injection or continuous
infusion. Formulations for injection may be presented in unit dosage form,
e.g., in ampules
or in mufti-dose containers, with an added preservative. The compositions may
take such
forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and
may contain
formulatory agents such as suspending, stabilizing and/or dispersing agents.
Pharmaceutical formulations for parenteral administration include aqueous
solutions
of the active compounds in water-soluble form. Additionally, suspensions of
the active
compounds may be prepared as appropriate oily injection suspensions. Suitable
lipophilic
solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty
acid esters, such
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77
as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions
may contain
substances which increase the viscosity of the suspension, such as sodium
carboxymethyl
cellulose, sorbitol, or dextran. Optionally, the suspension may also contain
suitable
stabilizers or agents which increase the solubility of the compounds to allow
for the
preparation of highly concentrated solutions. Alternatively, the active
ingredient may be in
powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-
free water, before
use.
The compounds may also be formulated in rectal compositions such as
suppositories
or retention enemas, e.g., containing conventional suppository bases such as
cocoa butter or
other glycerides. In addition to the formulations described previously, the
compounds may
also be formulated as a depot preparation. Such long acting formulations may
be
administered by implantation (for example subcutaneously or intramuscularly)
or by
intramuscular injection. Thus, for example, the compounds may be formulated
with suitable
polymeric or hydrophobic materials (for example as an emulsion in an
acceptable oil) or ion
exchange resins, or as sparingly soluble derivatives, for example, as a
sparingly soluble salt.
A pharmaceutical carrier for the hydrophobic compounds of the invention is a
co-
solvent system comprising benzyl alcohol, a nonpolar surfactant, a water-
miscible organic
polymer, and an aqueous phase. The co-solvent system may be the VPD co-solvent
system.
VPD is a solution of 3% w/v benzyl alcohol, 8% w/v of the nonpolar surfactant
polysorbate
80, and 65% w/v polyethylene glycol 300, made up to volume in absolute
ethanol. The VPD
co-solvent system (~PD:~W) consists of VPD diluted 1:1 v~ith a 5°/~
dextrose in water
solution. This co-solvent system dissolves hydrophobic compounds well, and
itself produces
low toxicity upon systemic administration. Naturally, the proportions of a co-
solvent system
may be varied considerably without destroying its solubility and toxicity
characteristics.
Furthermore, the identity of the co-solvent components may be varied: for
example, other
low-toxicity nonpolar surfactants may be used instead of polysorbate 80; the
fraction size of
polyethylene glycol may be varied; other biocompatible polymers may replace
polyethylene
glycol, e.g. polyvinyl pyrrolidone; and other sugars or polysaccharides may
substitute for
dextrose. Alternatively, other delivery systems for hydrophobic pharmaceutical
compounds
may be employed. Liposomes and emulsions are well known examples of delivery
vehicles
or carriers for hydrophobic drugs. Certain organic solvents such as
dimethylsulfoxide also
may be employed, although usually at the cost of greater toxicity.
Additionally, the
compounds may be delivered using a sustained-release system, such as
semipermeable
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7~
matrices of solid hydrophobic polymers containing the therapeutic agent.
Various types of
sustained-release materials have been established and are well known by those
skilled in the
art. Sustained-release capsules may, depending on their chemical nature,
release the
compounds for a few weeks up to over 100 days. Depending on the chemical
nature and the
biological stability of the therapeutic reagent, additional strategies for
protein or other active
ingredient stabilization may be employed.
The pharmaceutical compositions also may comprise suitable solid or gel phase
carriers or excipients. Examples of such carriers or excipients include but
are not limited to
calcium carbonate, calcium phosphate, various sugars, starches, cellulose
derivatives,
~ gelatin, and polymers such as polyethylene glycols. Many of the active
ingredients of the
invention may be provided as salts with pharmaceutically compatible counter
ions. Such
pharmaceutically acceptable base addition salts are those salts which retain
the biological
effectiveness and properties of the free acids and which are obtained by
reaction with
inorganic or organic bases such as sodium hydroxide, magnesium hydroxide,
ammonia,
trialkylamine, dialkylamine, monoalkylamine, dibasic amino acids, sodium
acetate,
potassium benzoate, tricthanol amine and the like.
The pharmaceutical composition of the invention may be in the form of a
complex of
the proteins) or other active ingredients) of present invention along with
protein or peptide
antigens. The protein and/or peptide antigen will deliver a stimulatory signal
to both B and T
lymphocytes. B lymphocytes will respond to antigen through their surface
immunoglobulin
receptor. T lymphocytes will respond to antigen through the T cell receptor
(TCIt)
following presentation of the antigen by MHO proteins. MHC and structurally
related
proteins including those encoded by class I and class II MHC genes on host
cells will serve
to present the peptide antigens) to T lymphocytes. The antigen components
could also be
supplied as purified MHC-peptide complexes alone or with co-stimulatory
molecules that
can directly signal T cells. Alternatively antibodies able to bind surface
immunoglobulin
and other molecules on B cells as well as antibodies able to bind the TCR and
other
molecules on T cells can be combined with the pharmaceutical composition of
the invention.
The pharmaceutical composition of the invention may be in the form of a
liposome in
which protein of the present invention is combined, in addition to other
pharmaceutically
acceptable tamers, with amphipathic agents such as lipids which exist in
aggregated form as
micelles, insoluble monolayers, liquid crystals, or lamellar layers in aqueous
solution.
Suitable lipids for liposomal formulation include, without limitation,
monoglycerides,
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diglycerides, sulfatides, lysolecithins, phospholipids, saponin, bile acids,
and the like.
Preparation of such liposomal formulations is within the level of skill in the
art, as disclosed,
for example, in U.S. Patent Nos. 4,235,871; 4,501,728; 4,837,028; and
4,737,323, all of
which are incorporated herein by reference.
The amount of protein or other active ingredient of the present invention in
the
pharmaceutical composition of the present invention will depend upon the
nature and
severity of the condition being treated, and on the nature of prior treatments
which the
patient has undergone. Ultimately, the attending physician will decide the
amount of protein
or other active ingredient of the present invention with which to treat each
individual patient.
Initially, the attending physician will administer low doses of protein or
other active
ingredient of the present invention and observe the patient's response. Larger
doses of
protein or other active ingredient of the present invention may be
administered until the
optimal therapeutic effect is obtained for the patient, and at that point the
dosage is not
increased further. It is contemplated that the various pharmaceutical
compositions used to
practice the method of the present invention should contain about 0.01 ~g to
about 100 mg
(preferably about 0.1 ~g to about 10 mg, more preferably about 0.1 ~g to about
1 mg) of
protein or other active ingredient of the present invention per kg body
weight. For
compositions of the present invention which are useful for bone, cartilage,
tendon or
ligament regeneration, the therapeutic method includes administering the
composition
topically, systematically, or locally as an implant or device. When
administered, the
therapeutic composition for use in this invention is, of course, in a pyrogen-
free,
physiologically acceptable form. Further, the composition may desirably be
encapsulated or
injected in a viscous form for delivery to the site of bone, cartilage or
tissue damage.
Topical administration may be suitable for wound healing and tissue repaix.
Therapeutically
useful agents other than a protein or other active ingredient of the invention
which may also
optionally be included in the composition as described above, may
alternatively or
additionally, be administered simultaneously or sequentially with the
composition in the
methods of the invention. Preferably for bone and/or cartilage formation, the
composition
would include a matrix capable of delivering the protein-containing or other
active
ingredient-containing composition to the site of bone andlor cartilage damage,
providing a
structure for the developing bone and cartilage and optimally capable of being
resorbed into
the body. Such matrices may be formed of materials presently in use fox other
implanted
medical applications.
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The choice of matrix material is based on biocompatibility, biodegradability,
mechanical properties, cosmetic appearance and interface properties. The
particular
application of the compositions will define the appropriate formulation.
Potential matrices
for the compositions may be biodegradable and chemically defined calcium
sulfate,
5 tricalcium phosphate, hydroxyapatite, polylactic acid, polyglycolic acid and
polyanhydrides.
Other potential materials are biodegradable and biologically well-defined,
such as bone or
dernzal collagen. Further matrices are comprised of pure proteins or
extracellular matrix
components. Other potential matrices are nonbiodegradable and chemically
defined, such as
sintered hydroxyapatite, bioglass, aluminates, or other cexamics. Matrices may
be comprised
10 of combinations of any of the above-mentioned types of material, such as
polylactic acid and
hydroxyapatite or collagen and tricalcium phosphate. The bioceramics may be
altered in
composition, such as in calcium-aluminate-phosphate and processing to alter
pore size,
particle size, particle shape, and biodegradability. Presently preferred is a
50:50 (mole
weight) copolymer of lactic acid and glycolic acid in the form of porous
particles having
15 diameters ranging from 150 to 800 microns. In some applications, it will be
useful to utilize
a sequestering agent, such as carboxymethyl cellulose or autologous blood
clot, to prevent
the protein compositions from disassociating from the matrix.
A preferred family of sequestering agents is cellulosic materials such as
alkylcelluloses (including hydroxyalkylcelluloses), including methylcellulose,
20 ethylcellulose, hydroxyethylcellulose, hydroxypropylcellulose,
hydroxypropyl-methylcellulose, and carbol~ymethylcellulose, the most preferred
being
cationic salts of carboxymethylcellulase (CMC). Other preferred sequestering
agents
include hyaluronic acid, sodium alginate, polyethylene glycol),
polyoxyethylene oxide,
carboxyvinyl polymer and polyvinyl alcohol). The amount of sequestering agent
useful
25 herein is 0.5-20 wt %, preferably 1-10 wt % based on total formulation
weight, which
represents the amount necessary to prevent desorption of the protein from the
polymer
matrix and to provide appropriate handling of the composition, yet not so much
that the
progenitor cells are prevented from infiltrating the matrix, thereby providing
the protein the
opportunity to assist the osteogenic activity of the progenitor cells. In
further compositions,
30 proteins or other active ingredients of the invention may be combined with
other agents
beneficial to the treatment of the bone andlor cartilage defect, wound, or
tissue in question.
These agents include various growth factors such as epidermal growth factor
(EGF), platelet
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81
derived growth factor (PDGF), transforming growth factors (TGF-oc and TGF-(3),
and
insulin-like growth factor (IGF).
The therapeutic compositions are also presently valuable for veterinary
applications.
Particularly domestic animals and thoroughbred horses, in addition to humans,
are desired
patients for such treatment with proteins or other active ingredients of the
present invention.
The dosage regimen of a protein-containing pharmaceutical composition to be
used in tissue
regeneration will be determined by the attending physician considering various
factors which
modify the action of the proteins, e.g., amount of tissue weight desired to be
formed, the site
of damage, the condition of the damaged tissue, the size of a wound, type of
damaged tissue
(e.g., bone), the patient's age, sex, and diet, the severity of any infection,
time of
administration and other clinical factors. The dosage may vary with the type
of matrix used
in the reconstitution and with inclusion of other proteins in the
pharmaceutical composition.
For example, the addition of other known growth factors, such as IGF I
(insulin like growth
factor I), to the final composition, may also effect the dosage. Progress can
be monitored by
periodic assessment of tissue/bone growth and/or repair, for example, X-rays,
histomorphomctric determinations and tetracycline labeling.
Polynucleotides of the present invention can also be used for gene therapy.
Such
polynucleotides can be introduced either in vivo or ex vivo into cells for
expression in a
mammalian subject. Polynucleotides of the invention may also be administered
by other
known methods for introduction of nucleic acid into a cell or organism
(including, without
limitation, in the form of viral vectors or naked D1~IA). Cells may also be
cultured ex vivo in
the presence of proteins of the present invention in order to proliferate or
to produce a
desired effect on or activity in such cells. Treated cells can then be
introduced in vivo for
therapeutic purposes.
4.12.3 EFFECTIVE DOSAGE
Pharmaceutical compositions suitable for use in the present invention include
compositions wherein the active ingredients are contained in an effective
amount to achieve
its intended purpose. More specifically, a therapeutically effective amount
means an amount
effective to prevent development of or to alleviate the existing symptoms of
the subject
being treated. Determination of the effective amount is well within the
capability of those
skilled in the art, especially in light of the detailed disclosure provided
herein. For any
compound used in the method of the invention, the therapeutically effective
dose can be
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~2
estimated initially from appropriate in vitro assays. For example, a dose can
be formulated in
animal models to achieve a circulating concentration range that can be used to
more
accurately determine useful doses in humans. For example, a dose can be
formulated in
animal models to achieve a circulating concentration range that includes the
ICso as
determined in cell culture (i.e., the concentration of the test compound which
achieves a
half maximal inhibition of the protein's biological activity). Such
information can be used
to more accurately determine useful doses in humans.
A therapeutically effective dose refers to that amount of the compound that
results in
amelioration of symptoms or a prolongation of survival in a patient. Toxicity
and therapeutic
efficacy of such compounds can be determined by standard pharmaceutical
procedures in
cell cultures or experimental animals, e.~., for determining the LDSo (the
dose lethal to 50%
of the population) and the EDso (the dose therapeutically effective in 50% of
the population).
The dose ratio between toxic and therapeutic effects is the therapeutic index
and it can be
expressed as the ratio between LDso and EDso. Compounds which exhibit high
therapeutic
indices are preferred. The data obtained from these cell culture assays and
animal studies
can be used in formulating a range of dosage for use in human. The dosage of
such
compounds lies preferably within a range of circulating concentrations that
include the EDSo
with little or no toxicity. The dosage may vary within this range depending
upon the dosage
form employed and the route of administration utilized. The exact formulation,
route of
administration and dosage can be chosen by the individual physician in view of
the patient's
condition. See, e.~., Fingl et al., 1759 in "The Pharmacol~gical basis of
'Therapeutics", Ch.
1 p.l . Dosage amount and interval may be adjusted individually to provide
plasma levels of
the active moiety which are sufficient to maintain the desired effects, or
minimal effective
concentration (MEC). The MEC will vary for each compound but can be estimated
from ira
vtt~°o data. Dosages necessary to achieve the MEC will depend on
individual characteristics
and route of administration. However, HPLC assays or bioassays can be used to
determine
plasma concentrations.
Dosage intervals can also be determined using MEC value. Compounds should be
administered using a regimen which maintains plasma levels above the MEC for
10-90% of
the time, preferably between 30-90% and most preferably between 50-90%. In
cases of local
administration or selective uptake, the effective local concentration of the
drug may not be
related to plasma concentration.
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83
An exemplary dosage regimen for polypeptides or other compositions of the
invention will be in the range of about 0.01 ~,g/kg to 100 mg/lcg of body
weight daily, with
the preferred dose being about 0.1 p,g/kg to 25 mg/kg of patient body weight
daily, varying
in adults and children. Dosing may be once daily, or equivalent doses may be
delivered at
longer or shorter intervals.
The amount of composition administered will, of course, be dependent on the
subject
being treated, on the subject's age and weight, the severity of the
affliction, the manner of
administration and the judgment of the prescribing physician.
4.12.4 PACKAGING
The compositions may, if desired, be presented in a pack or dispenser device
which
may contain one or more unit dosage forms containing the active ingredient.
The pack may,
for example, comprise metal or plastic foil, such as a blister pack. The pack
or dispenser
device may be accompanied by instructions for administration. Compositions
comprising a
compound of the invention formulated in a compatible pharmaceutical carrier
may also be
prepared, placed in an appropriate container, and labeled for treatment of an
indicated
condition.
4.13 ANTIBODIES
Also included in the invention are antibodies to proteins, or fragments of
proteins of
the lnvelltl~n. The term "antibody" as used herein refers to immunoglobulin
molecules and
immunologically active poutions of immunoglobulin (Ig) molecules, i.e.,
molecules that
contain an antigen-binding site that specifically binds (immunoreacts with) an
antigen. Such
antibodies include, but are not limited to, polyclonal, monoclonal, chimeric,
single chain,
Fib, Fab> and F~ab~)2 fragments, and an Fab expression library. In general, an
antibody molecule
obtained from humans relates to any of the classes IgG, IgM, IgA, IgE and IgD,
which differ
from one another by the nature of the heavy chain present in the molecule.
Certain classes
have subclasses as well, such as IgGI, IgG2, and others. Furthermore, in
humans, the light
chain may be a kappa chain or a lambda chain. Reference herein to antibodies
includes a
reference to all such classes, subclasses and types of human antibody species.
An isolated related protein of the invention may be intended to serve as an
antigen, or
a portion or fragment thereof, and additionally can be used as an immunogen to
generate
antibodies that immunospecifically bind the antigen, using standard techniques
for
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84
polyclonal and monoclonal antibody preparation. The full-length protein can be
used or,
alternatively, the invention provides antigenic peptide fragments of the
antigen for use as
immunogens. An antigenic peptide fragment comprises at least 6 amino acid
residues of the
amino acid sequence of the full length protein, such as an amino acid sequence
shown in
SEQ ID NO: 685-1368, or 1967-2564, or Tables 3A, 3B, 5, 7, or 8, and
encompasses an
epitope thereof such that an antibody raised against the peptide forms a
specific immune
complex with the full length protein or with any fragment that contains the
epitope.
Preferably, the antigenic peptide comprises at least 10 amino acid residues,
or at least 15
amino acid residues, or at least 20 amino acid residues, or at least 30 amino
acid residues.
Preferred epitopes encompassed by the antigenic peptide are regions of the
protein that are
located on its surface; commonly these are hydrophilic regions.
In certain embodiments of the invention, at least one epitope encompassed by
the
antigenic peptide is a surface region of the protein, e.g., a hydrophilic
region. A
hydrophobicity analysis of the human related protein sequence will indicate
which regions of
a related protein are particularly hydrophilic and, therefore, are likely to
encode surface
residues useful for targeting antibody production. As a means for targeting
antibody
production, hydropathy plots showing regions of hydrophilicity and
hydrophobicity may be
generated by any method well known in the art, including, for example, the
Kyte Doolittle or
the Hopp Woods methods, either with or without Fourier transformation. See,
e.g., Hopp and
Woods, 1981, Proc. Nat. Acad. Sci. USA 78: 3824-3828; I~yte and Doolittle
1982, J. Mol.
Biol. 157: 105-1429 each of which is incorporated herein by reference in its
entiret~r.
Antibodies that are specific for one or more domains within an antigenic
protein, or
derivatives, fragments, analogs or homologs thereof, are also provided herein.
A protein of the invention, or a derivative, fragment, analog, homolog or
ortholog
thereof, may be utilized as an immunogen in the generation of antibodies that
immunospecifically bind these protein components.
The term "specific for" indicates that the variable regions of the antibodies
of the
invention recognize and bind polypeptides of the invention exclusively (i.e.,
able to
distinguish the polypeptide of the invention from other similar polypeptides
despite sequence
identity, homology, or similarity found in the family of polypeptides), but
may also interact
with other proteins (for example, S. auf°eus protein A or other
antibodies in ELISA
techniques) through interactions with sequences outside the variable region of
the antibodies,
and in particular, in the constant region of the molecule. Screening assays to
determine
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binding specificity of an antibody of the invention are well known and
routinely practiced in
the art. For a comprehensive discussion of such assays, see Harlow et al.
(Eds), Antibodies
A Laboratory Manual; Cold Spring Harbor Laboratory; Cold Spring Harbor, NY
(1988),
Chapter 6. Antibodies that recognize and bind fragments of the polypeptides of
the
invention are also contemplated, provided that the antibodies are first and
foremost specific
for, as defined above, full-length polypeptides of the invention. As with
antibodies that are
specific for full length polypeptides of the invention, antibodies of the
invention that
recognize fragments are those which can distinguish polypeptides from the same
family of
polypeptides despite inherent sequence identity, homology, or similarity found
in the family
10 of proteins.
Antibodies of the invention are useful for, for example, therapeutic purposes
(by
modulating activity of a polypeptide of the invention), diagnostic puzposes to
detect or
quantitate a polypeptide of the invention, as well as purification of a
polypeptide of the
invention. Fits comprising an antibody of the invention for any of the
purposes described
15 herein are also comprehended. In general, a kit of the invention also
includes a control
antigen for which the antibody is immunospecific. The invention further
provides a
hybridoma that produces an antibody according to the invention. Antibodies of
the
invention are useful for detection and/or purification of the polypeptides of
the invention.
Monoclonal antibodies binding to the protein of the invention may be useful
20 diagnostic agents for the immunodetection of the protein. Neutralizing
monoclonal
antibodies binding to the protein may also be useful therapeutics for b~th
c~nditions
associated with the protein and also in the treatment of some forms ~f cancer
where
abn~rmal expression of the protein is involved. In the case of cancerous cells
or leukemic
cells, neutralizing monoclonal antibodies against the protein may be useful in
detecting and
25 preventing the metastatic spread of the cancerous cells, which may be
mediated by the
protein.
The labeled antibodies of the present invention can be used for izz vitro, lzz
vivo, and
izz situ assays t~ identify cells or tissues in which a fragment of the
polypeptide of interest is
expressed. The antibodies may also be used directly in therapies or other
diagnostics. The
30 present invention further provides the above-described antibodies
immobilized on a solid
support. Examples of such solid supports include plastics such as
polycarbonate, complex
carbohydrates such as agarose and Sepharose~, acrylic resins and such as
polyacrylamide
and latex beads. Techniques for coupling antibodies to such solid supports are
well known
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86
in the art (Weir, D.M. et al., "Handbook of Experimental Immunology" 4th Ed.,
Blackwell
Scientific Publications, Oxford, England, Chapter 10 (1986); Jacoby, W.D. et
al., Meth.
Enzym. 34 Academic Press, N.Y. (1974)). The immobilized antibodies of the
present
invention can be used for in vitro, in vivo, and in situ assays as well as for
immuno-affinity
purification of the proteins of the present invention.
Various procedures known within the art may be used for the production of
polyclonal or monoclonal antibodies directed against a protein of the
invention, or against
derivatives, fragments, analogs homologs or orthologs thereof (see, for
example, Antibodies:
A Laboratory Manual, Harlow E, and Lane D, 1988, Cold Spring Harbor Laboratory
Press,
Cold Spring Harbor, NY, incorporated herein by reference). Some of these
antibodies are
discussed below.
4.13.1 POLYCLONAL ANTIBODIES
For the production of polyclonal antibodies, various suitable host animals
(e.g.,
rabbit, goat, mouse or other mammal) may be immunized by one or more
injections with the
native protein, a synthetic variant thereof, or a derivative of the foregoing.
An appropriate
immunogenic preparation can contain, for example, the naturally occurring
immunogenic
protein, a chemically synthesized polypeptide representing the immunogenic
protein, or a
recombinantly expressed immunogenic protein. Furthermore, the protein may be
conjugated
to a second protein known to be immunogenic in the mammal being immunized.
Examples
of such immunogenic proteins include but are not limited to keyhole limpet
hemocyanin,
serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. The
preparation can
further include an adjuvant. Various adjuvants used to increase the
immunological response
include, but are not limited to, Freund's (complete and incomplete), mineral
gels (e.g.,
aluminum hydroxide), surface-active substances (e.g., lysolecithin, pluronic
polyols,
polyanions, peptides, oil emulsions, dinitrophenol, etc.), adjuvants usable in
humans such as
Bacille Calmette-Guerin and Corynebacterium parvum, or similar
immunostimulatory
agents. Additional examples of adjuvants that can be employed include MPL-TDM
adjuvant
(monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).
The polyclonal antibody molecules directed against the immunogenic protein can
be
isolated from the mammal (e.g., from the blood) and further purified by well
known
techniques, such as affinity chromatography using protein A or protein G,
which provide
primarily the IgG fraction of immune serum. Subsequently, or alternatively,
the specific
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87
antigen which is the target of the immunoglobulin sought, or an epitope
thereof, may be
immobilized on a column to purify the immune specific antibody by
immunoaf~nity
chromatography. Purification of immunoglobulins is discussed, for example, by
D.
Wilkinson (The Scientist, published by The Scientist, Inc., Philadelphia PA,
Vol. 14, No. 8
S (April 17, 2000), pp. 25-28).
4.13.2 MONOCLONAL ANTIBODIES
The term "monoclonal antibody" (MAb) or "monoclonal antibody composition", as
used herein, refers to a population of antibody molecules that contain only
one molecular
species of antibody molecule consisting of a unique light chain gene product
and a unique
heavy chain gene product. In particular, the complementarity determining
regions (CDRs)
of the monoclonal antibody are identical in all the molecules of the
population. MAbs thus
contain an antigen-binding site capable of immunoreacting with a particular
epitope of the
antigen characterized by a unique binding affinity for it.
Monoclonal antibodies can be prepared using hybridoma methods, such as those
described by Kohler and Milstein, Nature, 256, 495 (1975). In a hybridoma
method, a
mouse, hamster, ~r other appropriate h~st animal, is typically immunized with
an
immunizing agent to elicit lymphocytes that produce or are capable of
producing antibodies
that will specifically bind to the immunizing agent. Alternatively, the
lymphocytes can be
immunized in vitro.
The immunizing agent will typically include the protein antigen, a fragment
thereof
or a fusion protein thereof. Generally, either peripheral blood lymphocytes
are used if cells
of human origin are desired, or spleen cells or lymph node cells are used if
non-human
mammalian sources are desired. The lymphocytes are then fused with an
immortalized cell
line using a suitable fusing agent, such as polyethylene glycol, to form a
hybridoma cell
(Goding, Monocl~nal Antibodies: Principles and Practice, Academic Press,
(1986) pp. 59-
103). Immortalized cell lines are usually transformed mammalian cells,
particularly
myeloma cells of rodent, bovine and human origin. Usually, rat or mouse
myeloma cell
lines are employed. The hybridoma cells can be cultured in a suitable culture
medium that
preferably contains one or more substances that inhibit the growth or survival
of the unfused,
immortalized cells. For example, if the parental cells lack the enzyme
hypoxanthine guanine
phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the
hybridomas
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typically will include hypoxanthine, aminopterin, and thymidine ("HAT
medium"), which
substances prevent the growth of HGPRT-deficient cells.
Preferred immortalized cell lines are those that fuse efficiently, support
stable high
level expression of antibody by the selected antibody-producing cells, and are
sensitive to a
medium such as HAT medium. More preferred immortalized cell lines are murine
myeloma
lines, which can be obtained, for instance, from the Salk Institute Cell
Distribution Center,
San Diego, California and the American Type Culture Collection, Manassas,
Virginia.
Human myeloma and mouse-human heteromyeloma cell lines also have been
described for
the production of human monoclonal antibodies (Kozbor, J. Imrnunol., 133:3001
(1984);
Brodeur et al., Monoclonal Antibody Production Techniques and Applications,
Marcel
Dekker, Inc., New York, (1987) pp. 51-63).
The culture medium in which the hybridoma cells are cultured can then be
assayed
for the presence of monoclonal antibodies directed against the antigen.
Preferably, the
binding specificity of monoclonal antibodies produced by the hybridoma cells
is determined
by immunoprecipitation or by an in vitro binding assay, such as
radioimmunoassay (RIA) or
enzyme-linked immunoabsorbent assay (ELISA). Such tcclmiqucs and assays are
known in
the art. The binding affinity of the monoclonal antibody can, for example, be
determined by
the Scatchard analysis of Munson and Pollard, Anal. Biochem., 107, 220 (1980).
Preferably,
antibodies having a high degree of specificity and a high binding affinity for
the target
antigen are isolated.
After the desired hybridoma cells are identified, the clones can be subcloned
by
limiting dilution procedures and grown by standard meth~ds. Suitable culture
media f~r this
purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640
medium. Alternatively, the hybridoma cells can be grown in vivo as ascites in
a mammal.
The monoclonal antibodies secreted by the subclones can be isolated or
purified from
the culture medium or ascites fluid by conventional immunoglobulin
purification procedures
such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel
electrophoresis, dialysis, or affinity chromatography.
The monocl~nal antibodies can also be made by recombinant DNA methods, such as
those described in LT.S. Patent No. 4,816,567. DNA encoding the monoclonal
antibodies of
the invention can be readily isolated and sequenced using conventional
procedures (e.g., by
using oligonucleotide probes that are capable of binding specifically to genes
encoding the '
heavy and light chains of murine antibodies). The hybridoma cells of the
invention serve as
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89
a preferred source of such DNA. Once isolated, the DNA can be placed into
expression
vectors, which are then transfected into host cells such as simian COS cells,
Chinese hamster
ovary (CHO) cells, or myeloma cells that do not otherwise produce
imrnunoglobulin protein,
to obtain the synthesis of monoclonal antibodies in the recombinant host
cells. The DNA
also can be modified, for example, by substituting the coding sequence for
human heavy and
light chain constant domains in place of the homologous murine sequences (U.S.
Patent No.
4,816,567; Mornson, Nature 368, 812-13 (1994)) or by covalently joining to the
immunoglobulin coding sequence all or part of the coding sequence for a non-
immunoglobulin polypeptide. Such a non-immunoglobulin polypeptide can be
substituted
for the constant domains of an antibody of the invention, or can be
substituted for the
variable domains of one antigen-combining site of an antibody of the invention
to create a
chimeric bivalent antibody.
4.13.3 HUMANIZED ANTIBODIES
The antibodies directed against the protein antigens of the invention can
further
comprise humanized antibodies or human antibodies. These antibodies are
suitable for
administration to humans without engendering an immune response by the human
against
the administered immunoglobulin. Humani2ed forms of antibodies are chimeric
immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab,
Fab',
F(ab')2 or other antigen-binding subsequences of antibodies) that are
principally comprised
of the sequence of a human immunoglcbulin, and contain minimal sequence
derived from a
n~n-human immunoglobulin. Humanization can be performed following the method
of
Winter and co-workers (3ones et al., Nature, 321, 522-525 (1986); Riechmann et
al., Nature,
332, 323-327 (1988); Verhoeyen et al., Science, 239, 1534-1536 (1988)), by
substituting
rodent CDRs or CDR sequences for the corresponding sequences of a human
antibody. (See
also LT.S. Patent No. 5,225,539). In some instances, Fv framework residues of
the human
immunoglobulin are replaced by corresponding non-human residues. Humanized
antibodies
can also comprise residues that are found neither in the recipient antibody
nor in the
imported CDR or framework sequences. In general, the humanized antibody will
comprise
substantially all of at least one, and typically two, variable domains, in
which all or
substantially all of the CDR regions correspond to those of a non-human
immunoglobulin
and all or substantially all of the framework regions are those of a human
immunoglobulin
consensus sequence. The humanized antibody optimally also will comprise at
least a portion
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of an immunoglobulin constant region (Fc), typically that of a human
immunoglobulin
(Jones et al., 1986; Riechmann et al., 1988; and Presta, Curr. Op. Struct.
Biol., 2, 593-596
(1992)).
5 4.13.4 HUMAN ANTIBODIES
Fully human antibodies relate to antibody molecules in which essentially the
entire
sequences of both the light chain and the heavy chain, including the CDRs,
arise from
human genes. Such antibodies are termed "human antibodies", or "fully human
antibodies"
herein. Human monoclonal antibodies can be prepared by the trioma technique;
the human
10 B-cell hybridoma technique (see I~ozbor, et al., 1983 Immunol Today 4: 72)
and the EBV
hybridoma technique to produce human monoclonal antibodies (see Cole, et al.,
1985 In:
Monoclonal Antibodies and Cancer Thexapy, Alan R. Liss, Inc., pp. 77-96).
Human
monoclonal antibodies may be utilized in the practice of the present invention
and may be
produced by using human hybridomas (see Cote, et al., 1983. Proc Natl Acad Sci
USA 80,
15 2026-2030) or by transforming human B-cells with Epstein Barr Virus in
vitro (see Cole, et
al., 1985 In: Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc.,
pp. 77-96).
In addition, human antibodies can also be produced using additional
techniques,
including phage display libraries (Hoogenboom and Winter, J. Mol. Biol., 227,
381 (1991);
Marks et al., J. Mol. Biol., 222:581 (1991)). Similarly, human antibodies can
be made by
20 introducing human immunoglobulin loci into transgenic animals, e.g., mice
in which the
endogenous immunoglobulin genes have been partially or completely inactivated.
Upon
challenge, human antibody production is observed, which closely resembles that
seen in
humans in all respects, including gene rearrangement, assembly, and antibody
repertoire.
This approach is described, for example, in U.S. Patent Nos. 5,545,807;
5,545,806;
25 5,569,825; 5,625,126; 5,633,425; 5,661,016, and in Marks et al.
(Bio/Technology 10, 779-
783 (1992)); Lonberg et al. (Nature 368, 856-859 (1994)); Morrison (Nature
368, 812-13
(1994)); Fishwild et al, (Nature Biotechnology 14, 845-51 (1996)); Neuberger
(Nature
Biotechnology 14, 826 (1996)); and Lonberg and Huszar (Intern. Rev. Immunol.
13, 65-93
(1995)).
30 Human antibodies may additionally be produced using transgenic nonhuman
animals
that are modified so as to produce fully human antibodies rather than the
animal's
endogenous antibodies in response to challenge by an antigen. (See PCT
publication
W094/02602). The endogenous genes encoding the heavy and light immunoglobulin
chains
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91
in the nonhuman host have been incapacitated, and active loci encoding human
heavy and
light chain immunoglobulins are inserted into the host's genome. The human
genes are
incorporated, for example, using yeast artificial chromosomes containing the
requisite
human DNA segments. An animal which provides all the desired modiftcations is
then
obtained as progeny by crossbreeding intermediate transgenic animals
containing fewer than
the full complement of the modifications. The preferred embodiment of such a
nonhuman
animal is a mouse, and is termed the Xenomouse~ as disclosed in PCT
publications WO
96/33735 and WO 96/34096. This animal produces B cells that secrete fully
human
immunoglobulins. The antibodies can be obtained directly from the animal after
immunization with an immunogen of interest, as, for example, a preparation of
a polyclonal
antibody, or alternatively from immortalized B cells derived from the animal,
such as
hybridomas producing monoclonal antibodies. Additionally, the genes encoding
the
immunoglobulins with human variable regions can be recovered and expressed to
obtain the
antibodies directly, or can be further modified to obtain analogs of
antibodies such as, for
example, single chain Fv molecules.
An example of a method of producing a nonhuman host, exemplified as a mouse,
lacking expression of an endogenous immunoglobulin heavy chain is disclosed in
IJ.S.
Patent No. 5,939,598. It can be obtained by a method including deleting the J
segment genes
from at least one endogenous heavy chain locus in an embryonic stem cell to
prevent
rearrangement of the locus and to prevent formation of a transcript of a
rearranged
immunoglobulin heavy chain locus, the deletion being effected by a targeting
vector
containing a gene encoding a selectable markers and producing from the
embryonic stem cell
a transgenic mouse whose somatic and germ cells contain the gene encoding the
selectable
marker.
A method for producing an antibody of interest, such as a human antibody, is
disclosed in LT.S. Patent No. 5,916,771. It includes introducing an expression
vector that
contains a nucleotide sequence encoding a heavy chain into one mammalian host
cell in
culture, introducing an expression vector containing a nucleotide sequence
encoding a light
chain into another mammalian host cell, and fusing the two cells to form a
hybrid cell. The
hybrid cell expresses an antibody containing the heavy chain and the light
chain.
In a further improvement on this procedure, a method for identifying a
clinically
relevant epitope on an immunogen, and a correlative method for selecting an
antibody that
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binds immunospecifically to the relevant epitope with high affinity, are
disclosed in PCT
publication WO 99/53049.
4.13.5 FAB FRAGMENTS AND SINGLE CHAIN ANTIBODIES
According to the invention, techniques can be adapted for the production of
single-chain antibodies specific to an antigenic protein of the invention (see
e.g., U.S. Patent
No. 4,946,778). In addition, methods can be adapted for the construction of
Fab expression
libraries (see e.g., Huse, et al., 1989 Science 246, 1275-1281) to allow rapid
and effective
identification of monoclonal Fab fragments with the desired specificity for a
protein or
derivatives, fragments, analogs or homologs thereof. Antibody fragments that
contain the
idiotypes to a protein antigen may be produced by techniques known in the art
including, but
not limited to: (i) an F(ab')2 fragment produced by pepsin digestion of an
antibody molecule;
(ii) an Fab fragment generated by reducing the disulfide bridges of an F~ab~~2
fragment; (iii) an
Fab fragment generated by the treatment of the antibody molecule with papain
and a reducing
agent and (iv) F~ fragments.
4.13.6 BISPECIFIC ANTIBODIES
Bispecific antibodies are monoclonal, preferably human or humanized,
antibodies
that have binding specificities for at least two different antigens. In the
present case, one of
the binding specificities is for an antigenic protein of the invention. The
second binding
target is any other antigen, and advantageously is a cell-surface protein or
receptor or
receptor subunit.
Methods for making bispecific antibodies are known in the art. Traditionally,
the
recombinant production of bispecific antibodies is based on the co-expression
of two
immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have
different
specificities (Milstein and Cuello, Nature, 305, 537-539 (1983)). Because of
the random
assortment of immunoglobulin heavy and light chains, these hybridomas
(quadromas)
produce a potential mixture of ten different antibody molecules, of which only
one has the
correct bispecific structure. The purification of the correct molecule is
usually accomplished
by affinity chromatography steps. Similar procedures are disclosed in WO
93/08829,
published 13 May'1993, and in Traunecker et al., 1991 EMBO J., 10, 3655-3659.
Antibody variable domains with the desired binding specificities (antibody-
antigen
combining sites) can be fused to immunoglobulin constant domain sequences. The
fusion
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preferably is with an immunoglobulin heavy-chain constant domain, comprising
at least part
of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-
chain constant
region (CH1) containing the site necessary for light-chain binding present in
at least one of
the fusions. DNAs encoding the immunoglobulin heavy-chain fusions and, if
desired, the
immunoglobulin light chain, are inserted into separate expression vectors, and
are co-
transfected into a suitable host organism. For further details of generating
bispecific
antibodies see, for example, Suresh et al., Methods in Enzymology, 121, 210
(1986).
According to another approach described in WO 96!27011, the interface between
a
pair of antibody molecules can be engineered to maximize the percentage of
heterodimers
that are recovered from recombinant cell culture. The preferred interface
comprises at least
a part of the CH3 region of an antibody constant domain. In this method, one
or more small
amino acid side chains from the interface of the first antibody molecule are
replaced with
larger side chains (e.g. tyrosine or tryptophan). Compensatory "cavities" of
identical or
similar size to the large side chains) are created on the interface of the
second antibody
molecule by replacing large amino acid side chains with smaller ones (e.g.
alanine or
threonine). This provides a mechanism for increasing the yield of the
heterodimer over other
unwanted end-products such as homodimers.
Eispeci~c antibodies can be prepared as full-length antibodies or antibody
fragments
(e.g. F(ab')2 bispecific antibodies). Techniques for generating bispecific
antibodies from
antibody fragments have been described in the literature. For example,
bispecific antibodies
can be prepared using chemical linl~age. l3rennan et al., Science 229, 81
(1985) describe a
procedure wherein intact antibodies are proteolytically cleaved to generate
F(ab')2
fragments. These fragments are reduced in the presence of the dithiol
complexing agent
sodium arsenite to stabilize vicinal dithiols and prevent intermolecular
disulfide formation.
The Fab' fragments generated are then converted to thionitrobenzoate (TNB)
derivatives.
One of the Fab'-TNB derivatives is then reconverted to the Fab'-thiol by
reduction with
mercaptoethylamine and is mixed with an equimolar amount of the other Fab'-TNB
derivative to form the bispecific antibody. The bispecific antibodies produced
can be used
as agents for the selective immobilization of enzymes.
Additionally, Fab' fragments can be directly recovered from E. coli and
chemically
coupled to form bispecific antibodies. Shalaby et al., J. Exp. Med, 175, 217-
225 (1992)
describe the production of a fully humanized bispecific antibody F(ab')2
molecule. Each
Fab' fragment was separately secreted from E. coli and subjected to directed
chemical
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94
coupling in vitro to form the bispecific antibody. The bispecific antibody
thus formed was
able to bind to cells overexpressing the ErbB2 receptor and normal human T
cells, as well as
trigger the lytic activity of human cytotoxic lymphocytes against human breast
tumor targets.
Various techniques for making and isolating bispecifrc antibody fragments
directly
from recombinant cell culture have also been described. For example,
bispecific antibodies
have been produced using leucine zippers. I~ostelny et al., J. Immunol.
148(5), 1547-1553
(1992). The leucine zipper peptides from the Fos and Jun proteins were linked
to the Fab'
portions of two different antibodies by gene fusion. The antibody homodimers
were reduced
at the hinge region to form monomers and then re-oxidized to form the antibody
heterodimers. This method can also be utilized for the production of antibody
homodimers.
The "diabody" technology described by Hollinger et al., Proc. Natl. Acad. Sci.
USA 90,
6444-6448 (1993) has provided an alternative mechanism for making bispecific
antibody
fragments. The fragments comprise a heavy-chain variable domain (VH) connected
to a
light-chain variable domain (VL) by a linker which is too short to allow
pairing between the
two domains on the same chain. Accordingly, the VH and VL domains of one
fragment are
forced to pair with the complementary VL and VH domains of another fragment,
thereby
forming two antigen-binding sites. Another strategy for making bispecific
antibody
fragments by the use of single-chain Fv (sFv) dimers has also been reported.
See, Gruber et
al., J. Immunol. 152, 5368 (1994).
Antibodies with more than two valencies are contemplated. For example,
trispecific
antibodies can be prepared. Tutt et al., J. Immunol. 147 60 (1991).
E<~emplary bispecific antibodies can bind to two different epitopes, at least
one of
which originates in the protein antigen of the invention. Alternatively, an
anti-antigenic ann
of an immunoglobulin molecule can be combined with an arm which binds to a
triggering
molecule on a leukocyte such as a T-cell receptor molecule (e.g. CD2, CD3,
CD28, or B7),
or Fc receptors for IgG (FcyR), such as FcyRI (CD64), FcyRII (CD32) and
FcyRIII (CD16)
so as to focus cellular defense mechanisms to the cell expressing the
particular antigen.
Bispecific antibodies can also be used to direct cytotoxic agents to cells
which express a
particular antigen. These antibodies possess an antigen-binding arm and an arm
which binds
a cytotoxic agent or a radionuclide chelator, such as EOTUBE, DPTA, DOTA, or
TETA.
Another bispeciBc antibody of interest binds the protein antigen described
herein and further
binds tissue factor (TF).
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4.13.7 HETEROCONJUGATE ANTIBODIES
Heteroconjugate antibodies are also within the scope of the present invention.
Heteroconjugate antibodies are composed of two covalently joined antibodies.
Such
antibodies have, for example, been proposed to target immune system cells to
unwanted cells
5 (IT.S. Patent No. 4,676,980), and for treatment of HIV infection (WO
91/00360; WO
92/200373; EP 03089). It is contemplated that the antibodies can be prepared
in vitro using
known methods in synthetic protein chemistry, including those involving
crosslinking
agents. For example, immunotoxins can be constructed using a disulfide
exchange reaction
or by forming a thioether bond. Examples of suitable reagents for this purpose
include
10 iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for
example, in U.S.
Patent No. 4,676,980.
4.13.8 EFFECTOR FUNCTION ENGINEERING
It can be desirable to modify the antibody of the invention with respect to
effector
15 function, so as to enhance, e.g., the effectiveness of the antibody in
treating cancer. For
example, cysteine residues) can be introduced into the Fc region, thereby
allowing
interchain disulfide bond formation in this region. The homodimeric antibody
thus
generated can have improved internalization capability and/or increased
complement-
mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See
Caron et
20 al., J. Exp Med., 176, 1191-1195 (1992) and Shopes, J. Immunol., 148, 2918-
2922 (1992).
Homodimeric antibodies with enhanced anti-tumor activity can also be prepared
using
heterobifunctional cross-linkers as described in Wolff et al. Cancer
Pvesearch, 53, 2560-
2565 (1993). Alternatively, an antibody can be engineered that has dual Fc
regions and can
thereby have enhanced complement lysis and ADCC capabilities. See Stevenson et
al.,
25 Anti-Cancer Drug Design, 3, 219-230 (1989).
4.13.9 IMMiJNOCONJUGATES
The invention also peutains to immunoconjugates comprising an antibody
conjugated
to a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g., an
enzymatically active
30 toxin of bacterial, fungal, plant, or animal origin, or fragments thereof),
or a radioactive
isotope (i.e., a radioconjugate).
Chemotherapeutic agents useful in the generation of such immunoconjugates have
been described above. Enzymatically active toxins and fragments thereof that
can be used
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include diphtheria A chain, nonbinding active fragments of diphtheria toxin,
exotoxin A
chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A
chain,
alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca
americana proteins
(PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin,
sapaonaria
officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin,
enomycin, and the
tricothecenes. A variety of radionuclides are available for the production of
radioconjugated
antibodies. Examples include zl2Bi, 1311, l3iln, goY, and 186Re.
Conjugates of the antibody and cytotoxic agent are made using a variety of
bifunctional protein-coupling agents such as N-succinimidyl-3-(2-
pyridyldithiol) propionate
(SPDP), iminothiolane (IT), bifunctional derivatives of imidoesters (such as
dirnethyl
adipimidate HCL), active esters (such as disuccinimidyl suberate), aldehydes
(such as
glutareldehyde), bis-azido compounds (such as bis (p-azidobenzoyl)
hexanediamine), bis-
diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine),
diisocyanates
(such as tolyene 2,6-diisocyanate), and bis-active fluorine compounds (such as
1,5-difluoro-
2,4-dinitrobenzene). For example, a ricin immunotoxin can be prepared as
described in
Vitetta et al., Science, 238: 1098 (1987). Carbon-14-labeled 1-
isothi~cyanatobenzyl-3-
methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chclating
agent for
conjugation of radionucleotide to the antibody. Sec WO94/11026.
In another embodiment, the antibody can be conjugated to a "receptor" (such
streptavidin) for utilization in tumor pretargeting wherein the antibody-
receptor conjugate is
administered to the patient, followed by removal of unbound ca~njugatc from
the circulation
using a clearing agent and then administration of a "ligand" (e.g., avidin)
that is in turn
c~njugated t~ a cytotoxic agent.
4.14 COMPUTER READABLE SEQUENCES
In one application of this embodiment, a nucleotide sequence of the present
invention
can be recorded on computer readable media. As used herein, "computer readable
media"
refers to any medium which can be read and accessed directly by a computer.
Such media
include, but are not limited to: magnetic storage media, such as floppy discs,
hard disc
storage medium, and magnetic tape; optical storage media such as CD-ROM;
electrical
storage media such as RAM and ROM; and hybrids of these categories such as
magnetic/optical storage media. A skilled artisan can readily appreciate how
any of the
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presently known computer readable mediums can be used to create a manufacture
comprising computer readable medium having recorded thereon a nucleotide
sequence of the
present invention. As used herein, "recorded" refers to a process for storing
information on
computer readable medium. A skilled artisan can readily adopt any of the
presently known
methods for recording information on computer readable medium to generate
manufactures
comprising the nucleotide sequence information of the present invention.
A variety of data storage structures are available to a skilled artisan for
creating a
computer readable medium having recorded thereon a nucleotide sequence of the
present
invention. The choice of the data storage structure will generally be based on
the means
chosen to access the stored information. In addition, a variety of data
processor programs
and formats can be used to store the nucleotide sequence information of the
present
invention on computer readable medium. The sequence information can be
represented in a
word processing text file, formatted in commercially-available software such
as WordPerfect
and Microsoft Word, or represented in the form of an ASCII file, stored in a
database
application, such as DB2, Sybase, Oracle, or the like. A skilled artisan can
readily adapt any
number of data processor structuring formats (e.~. text ftle or database) in
order to obtain
computer readable medium having recorded thereon the nucleotide sequence
information of
the present invention.
By providing any of the nucleotide sequences SEQ ID NO: 1-684, or 1369-1966 or
a
representative fragment thereof; or a nucleotide sequence at least 95%
identical to any of the
nucleotide sequences of SEQ ID INTO: 1-684, or 1369-1966 in computer readable
form, a
skilled artisan can routinely access the sequence information for a variety of
purposes.
Computer software is publicly available which allows a skilled artisan to
access sequence
information provided in a computer readable medium. The examples which follow
demonstrate how software which implements the BLAST (Altschul et al., J. Mol.
Biol.
215:403-410 (1990)) and BLAZE (Brutlag et al., Comp. Chem. 17:203-207 (1993))
search
algorithms on a Sybase system is used to identify open reading frames (ORFs)
within a
nucleic acid sequence. Such ORFs may be protein-encoding fragments and may be
useful in
producing commercially important proteins such as enzymes used in fermentation
reactions
and in the production of commercially useful metabolites.
As used herein, "a computer-based system" refers to the hardware means,
software
means, and data storage means used to analyze the nucleotide sequence
information of the
present invention. The minimum hardware means of the computer-based systems of
the
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present invention comprises a central processing unit (CPU), input means,
output means, and
data storage means. A skilled artisan can readily appreciate that any one of
the currently
available computer-based systems are suitable for use in the present
invention. As stated
above, the computer-based systems of the present invention comprise a data
storage means
having stored therein a nucleotide sequence of the present invention and the
necessary
hardware means and software means for supporting and implementing a search
means. As
used herein, "data storage means" refers to memory which can store nucleotide
sequence
information of the present invention, or a memory access means which can
access
manufactures having recorded thereon the nucleotide sequence information of
the present
invention.
As used herein, "search means" refers to one or more programs which are
implemented on the computer-based system to compare a target sequence or
target structural
motif with the sequence information stored within the data storage means.
Search means are
used to identify fragments or regions of a known sequence which match a
particular target
sequence or target motif A variety of known algorithms are disclosed publicly
and a variety
of commercially available software for conducting search means arc and can be
used in the
computer-based systems of the present invention. Examples of such software
includes, but
is not limited to, Smith-Waterman, lVIacPattcrn (EMBL), )3LASTN and 13LASTA
(NP~LYPEPTIDEIA). A skilled artisan can readily recognize that any one of the
available
algorithms or implementing software packages for conducting homology searches
can be
adapted for use in the present computer-based systems. As used herein, a
"target sequence"
can be any nucleic acid or amino acid sequence of six or more nucleotides or
two or more
amino acids. A skilled artisan can readily recognize that the longer a target
sequence is, the
less likely a target sequence will be present as a random occurrence in the
database. The
most preferred sequence length of a target sequence is from about 10 to 300
amino acids,
more preferably from about 30 to 100 nucleotide residues. However, it is well
recognized
that searches for commercially important fragments, such as sequence fragments
involved in
gene expression and protein processing, may be of shorter length.
As used herein, "a target structural motif," or "target motif," refers to any
rationally
selected sequence or combination of sequences in which the sequences) are
chosen based on
a three-dimensional configuration which is formed upon the folding of the
target motif.
There are a variety of target motifs knowxn in the art. Protein target motifs
include, but are
not limited to, enzyme active sites and signal sequences. Nucleic acid target
motifs include,
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but are not limited to, promoter sequences, hairpin structures and inducible
expression
elements (protein binding sequences).
4.15 TRIPLE HELIX FORMATION
In addition, the fragments of the present invention, as broadly described, can
be used
to control gene expression through triple helix formation or antisense DNA or
RNA, both of
which methods are based on the binding of a polynucleotide sequence to DNA or
RNA.
Polynucleotides suitable for use in these methods are preferably 20 to 40
bases in length and
are designed to be complementary to a region of the gene involved in
transcription (triple
helix-see Lee et al., Nucl. Acids Res. 6, 3073 (1979); Cooney et al., Science
15241, 456
(1988); and Dervan et al., Science 251, 1360 (1991)) or to the mRNA itself
(antisense-
~hnno, J. Neurochem. 56:560 (1991); ~ligodeoxynucleotides as Antisense
Inhibitors of
Gene Expression, CRC Press, Boca Raton, FL (1988)). Triple helix-formation
optimally
results in a shut-off of RNA transcription from DNA, while antisense RNA
hybridization
blocks translation of an mRNA molecule into polypeptide. Both techniques have
been
demonstrated to be effective in model systems. Inforniation contained in the
sequences of
the present invention is necessary for the design of an antisense or triple
helix
oligonucleotide.
4.16 DIAGNOSTIC ASSAYS AND KITS
The present invention further provides methods to identify the presence or
expression
of one of the ~RFs of the present invention, or homolog thereof, in a test
sample, using a
nucleic acid probe or antibodies of the present invention, optionally
conjugated or otherwise
associated with a suitable label.
In general, methods for detecting a polynucleotide of the invention can
comprise
contacting a sample with a compound that binds to and forms a complex with the
polynucleotide for a period sufficient to form the complex, and detecting the
complex, so
that if a complex is detected, a polynucleotide of the invention is detected
in the sample.
Such methods can also comprise contacting a sample under stringent
hybridization
conditions with nucleic acid primers that anneal to a polynucleotide of the
invention under
such conditions, and amplifying annealed polynucleotides, so that if a
polynucleotide is
ampliEed, a polynucleotide of the invention is detected in the sample.
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In general, methods for detecting a polypeptide of the invention can comprise
contacting a sample with a compound that binds to and forms a complex with the
polypeptide for a period sufficient to form the complex, and detecting the
complex, so that if
a complex is detected, a polypeptide of the invention is detected in the
sample.
In detail, such methods comprise incubating a test sample with one or more of
the
antibodies or one or more of the nucleic acid probes of the present invention
and assaying
for binding of the nucleic acid probes or antibodies to components within the
test sample.
Conditions for incubating a nucleic acid probe or antibody with a test sample
vary.
Incubation conditions depend on the format employed in the assay, the
detection methods
employed, and the type and nature of the nucleic acid probe or antibody used
in the assay.
~ne skilled in the art will recognize that any one of the commonly available
hybridization,
amplification or immunological assay formats can readily be adapted to employ
the nucleic
acid probes or antibodies of the present invention. Examples of such assays
can be found in
Chard, T., An Introduction to Radioimmunoassay and Related Techniques,
Elsevier Science
Publishers, Amsterdam, The Netherlands (1986); Bullock, G.R. et al.,
Techniques in
Immunocytochemistry, l~cademic Press, ~rlando, FL Vol. 1 (1982), Vol. 2
(1983), Vol. 3
(1985); Tijssen, P., Practice and Theory of immunoassays: Laboratory
Techniques in
Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam,
The
Netherlands (1985). The test samples of the present invention include cells,
protein or
membrane extracts of cells, or biological fluids such as sputum, blood, serum,
plasma, or
urine. The test sample used in the above-described method will vary based on
the assay
format, nature of the detection method and the tissues, cells or extracts used
as the sample to
be assayed. Methods for preparing protein extracts or membrane extracts of
cells are well
known in the art and can be readily be adapted in order to obtain a sample
which is
compatible with the system utilized.
In another embodiment of the present invention, kits are provided which
contain the
necessary reagents to carry out the assays of the present invention.
Specifically, the
invention provides a compartment kit to receive, in close confinement, one or
more
containers which comprises: (a) a first container comprising one of the probes
or antibodies
of the present invention; and (b) one or more other containers comprising one
or more of the
following: wash reagents, reagents capable of detecting presence of a bound
probe or
antibody.
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In detail, a compartment kit includes any kit in which reagents are contained
in
separate containers. Such containers include small glass containers, plastic
containers or
strips of plastic or paper. Such containers allows one to efEciently transfer
reagents from
one compartment to another compartment such that the samples and reagents are
not
cross-contaminated, and the agents or solutions of each container can be added
in a
quantitative fashion from one compartment to another. Such containers will
include a
container which will accept the test sample, a container which contains the
antibodies used
in the assay, containers which contain wash reagents (such as phosphate
buffered saline,
Tris-buffers, etc.), and containers which contain the reagents used to detect
the bound
antibody or probe. Types of detection reagents include labeled nucleic acid
probes, labeled
secondary antibodies, or in the alternative, if the primary antibody is
labeled, the enzymatic,
or antibody binding reagents which are capable of reacting with the labeled
antibody. One
skilled in the art will readily recognize that the disclosed probes and
antibodies of the present
invention can be readily incorporated into one of the established kit formats
which are well
kn~wn in the art.
4.17 IDI~AI. Il~IA~ING
The novel polypeptides and binding partners of the invention are useful in
medical
imaging of sites expressing the molecules of the invention (e.g., where the
polypeptide of the
invention is involved in the immune response, for imaging sites of
inflammation or
infection). See, e.g., I~:unkel et al., U.S. Pat. hTO. 5,413,778. Such methods
involve
cheanical attachment of a labeling ~r imaging agent, administration of the
labeled
polypeptide to a subject in a pharmaceutically acceptable carrier, and imaging
the labeled
polypeptide in viv~ at the target site.
4.18 SCREENING ASSAYS
Using the isolated proteins and p~lynucleotides of the invention, the present
invention further provides methods of obtaining and identifying agents which
bind to a
polypeptide encoded by an ORF corresponding to any of the nucleotide sequences
set forth
in SEQ ID NO: 1-684, or 1369-1966, or bind to a specific domain of the
polypeptide
encoded by the nucleic acid. In detail, said method comprises the steps of:
(a) contacting an agent with an isolated protein encoded by an ORF of the
present invention, or nucleic acid of the invention; and
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(b) determining whether the agent binds to said protein or said nucleic acid.
In general, therefore, such methods for identifying compounds that bind to a
polynucleotide of the invention can comprise contacting a compound with a
polynucleotide
of the invention for a time sufficient to form a polynucleotide/compound
complex, and
detecting the complex, so that if a polynucleotide/compound complex is
detected, a
compound that binds to a polynucleotide of the invention is identified.
Likewise, in general, therefore, such methods for identifying compounds that
bind to
a polypeptide of the invention can comprise contacting a compound with a
polypeptide of
the invention for a time sufficient to form a polypeptide/compound complex,
and detecting
the complex, so that if a polypeptide/compound complex is detected, a compound
that binds
to a polynucleotide of the invention is identified.
Methods for identifying compounds that bind to a polypeptide of the invention
can
also comprise contacting a compound with a polypeptide of the invention in a
cell for a time
sufficient to form a polypeptide/compound complex, wherein the complex drives
expression
of a receptor gene sequence in the cell, and detecting the complex by
detecting reporter gene
sequence expression, so that if a polypeptide/compound complex is detected, a
compound
that binds a polypeptide of the invention is identified.
Compounds identified via such methods can include compounds which modulate the
activity of a polypeptide of the invention (that is, increase or decrease its
activity, relative to
activity observed in the absence of the compound). Alternatively, compounds
identified via
such methods can include compounds which modulate the expression of a
polynucleotide of
the invention (that is, increase or decrease expression relative to expression
levels observed
in the absence of the compound). Compounds, such as compounds identified via
the
methods of the invention, can be tested using standard assays well known to
those of skill in
the art for their ability to modulate activity/expression.
The agents screened in the above assay can be, but are not limited to,
peptides,
carbohydrates, vitamin derivatives, or other pharmaceutical agents. The agents
can be
selected and screened at random or rationally selected or designed using
protein modeling
techniques.
For random screening, agents such as peptides, carbohydrates, pharmaceutical
agents
and the like are selected at random and are assayed for their ability to bind
to the protein
encoded by the ORF of the present invention. Alternatively, agents may be
rationally
selected or designed. As used herein, an agent is said to be "rationally
selected or designed"
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when the agent is chosen based on the configuration of the particular protein.
For example,
one skilled in the art can readily adapt currently available procedures to
generate peptides,
pharniaceutical agents and the like, capable of binding to a specific peptide
sequence, in
order to generate rationally designed antipeptide peptides, for example see
Hurby et al.,
Application of Synthetic Peptides: Antisense Peptides," In Synthetic Peptides,
A User's
Guide, W.H. Freeman, NY (1992), pp. 289-307, and Kaspczak et al., Biochemistry
28:9230-8 (1989), or pharmaceutical agents, or the like.
In addition to the foregoing, one class of agents of the present invention, as
broadly
described, can be used to control gene expression through binding to one of
the ORFs or
EMFs of the present invention. As described above, such agents can be randomly
screened
or rationally designedlselected. Targeting the ORF or EMF allows a skilled
artisan to design
sequence specific or element specific agents, modulating the expression of
either a single
ORF or multiple ORFs which rely on the same EMF for expression control. One
class of
DNA binding agents are agents which contain base residues which hybridize or
form a triple
helix formation by binding to DNA or RNA. Such agents can be based on the
classic
phosphodiester, ribonucleic acid backbone, or can be a variety of sulfhydryl
or polymeric
derivatives which have base attachment capacity.
Agents suitable for use in these methods preferably contain 20 to 40 bases and
are
designed to be complementary to a region of the gene involved in transcription
(triple helix -
see Lee et al., Nucl. Acids Res. 6, 3073 (1979); Cooney et al., Science 241,
456 (1988); and
Dervan et al., Science 251, 1360 (1991)) or to the mRNA itself (antisense-
OkaIl~, J.
Neurochem. 56, 560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of
Gene
Expression, CRC Press, Boca Raton, FL (1988)). Triple helix-formation
optimally results in
a shut-off of RNA transcription from DNA, while antisense RNA hybridization
blocks
translation of an mRNA molecule into polypeptide. Both techniques have been
demonstrated to be effective in model systems. Information contained in the
sequences of
the present invention is necessary for the design of an antisense or triple
helix
oligonucleotide and other DNA binding agents.
Agents which bind to a protein encoded by one of the ORFs of the present
invention
can be used as a diagnostic agent. Agents which bind to a protein encoded by
one of the
ORFs of the present invention can be formulated using known techniques to
generate a
pharmaceutical composition.
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4.19 USE OF NUCLEIC ACIDS AS PROBES
Another aspect of the subject invention is to provide for polypeptide-specific
nucleic
acid hybridization probes capable of hybridizing with naturally occurnng
nucleotide
sequences. The hybridization probes of the subject invention may be derived
from any of
the nucleotide sequences SEQ ID NO: 1-684, or 1369-1966. Because the
corresponding
gene is only expressed in a limited number of tissues, a hybridization probe
derived from
any of the nucleotide sequences SEQ ID NO: 1-684, or 1369-1966 can be used as
an
indicator of the presence of RNA of cell type of such a tissue in a sample.
Any suitable hybridization technique can be employed, such as, for example, in
situ
hybridization. PCR as described in US Patents Nos. 4,683,195 and 4,965,188
provides
additional uses for oligonucleotides based upon the nucleotide sequences. Such
probes used
in PCR may be of recombinant origin, may be chemically synthesized, or a
mixture of both.
The probe will comprise a discrete nucleotide sequence for the detection of
identical
sequences or a degenerate pool of possible sequences for identiEcation of
closely related
genomic sequences.
Other means for producing speciEc hybridization probes for nucleic acids
include the
cloning of nucleic acid sequences into vectors for the production of mRNA
probes. Such
vectors are known in the art and are commercially available and may be used to
synthesize
RNA probes irt vitro by means of the addition of the appropriate RNA
polymerise as T7 or
SP6 RNA polymerise and the appropriate radioactively labeled nucleotides. The
nucleotide
sequences may be used to construct hybridization probes for mapping their
respective
genomic sequences. The nucleotide sequence provided herein may be mapped to a
chromosome or specific regions of a chromosome using well-known genetic and/or
chromosomal mapping techniques. These techniques include in situ
hybridization, linkage
analysis against known chromosomal markers, hybridization screening with
libraries or
flow-sorted chromosomal preparations specific to known chromosomes, and the
like. The
technique of fluorescent in situ hybridization of chromosome spreads has been
described,
among other places, in Verma et al (1988) Human Chromosomes: A Manual of Basic
Techniques, Pergamon Press, New York NY.
Fluorescent ifa situ hybridization of chromosomal preparations and other
physical
chromosome mapping techniques may be correlated with additional genetic map
data.
Examples of genetic map data can be found in the 1994 Genome Issue of Science
(265:1981 f). Correlation between the location of a nucleic acid on a physical
chromosomal
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map and a specific disease (or predisposition to a specific disease) may help
delimit the
region of DNA associated with that genetic disease. The nucleotide sequences
of the subject
invention may be used to detect differences in gene sequences between normal,
carrier or
affected individuals.
4.20 PREPARATION OF SUPPORT BOUND OLIGONUCLEOTIDES
Oligonucleotides, i.e., small nucleic acid segments, may be readily prepared
by, for
example, directly synthesizing the oligonucleotide by chemical means, as is
commonly
practiced using an automated oligonucleotide synthesizer.
Support bound oligonucleotides may be prepared by any of the methods known to
those
of skill in the art using any suitable support such as glass, polystyrene or
Teflon. One strategy
is to precisely spot oligonucleotides synthesized by standard synthesizers.
Immobilization can
be achieved using passive adsorption (Inouye ~ Hondo, (1990) J. Clin.
Microbiol. 28(6), 1469-
72); using LTV light (Nagata et al., 1985; Dahlen et al., 1987; Morrissey ~
Collins, (1989) Mol.
Cell Probes 3(2) 189-207) or by covalent binding of base modified DNA (I~eller
et al., 1988;
1989); all references being specifically incorporated herein.
Another strategy that may be employed is the use of the strong biotin-
streptavidin
interaction as a linker. For example, Broude et al. (1994) Proc. Natl. Acad.
Sci. LJSA 91(8),
3072-6, describe the use of biotinylated probes, although these are duplex
probes, that are
immobilized on streptavidin-coated magnetic beads. Streptavidin-coated beads
may be
purchased from Dynal, Oslo. Of course, this same linking chemistry is
applicable to coating
any surface with streptavidin. Biotinylated probes may be purchased from
various sources,
such as, e.g., Operon Technologies (Alameda, CA).
Nunc Laboratories (Naperville, IL) is also selling suitable material that
could be used.
Nunc Laboratories have developed a method by which DNA can be covalently bound
to the
microwell surface termed Covalink NH. CovaLink NH is a polystyrene surface
grafted with
secondary amino groups (>NH) that serve as bridgeheads for further covalent
coupling.
CovaLink Modules may be purchased from Nunc Laboratories. DNA molecules may be
bound
to CovaLink exclusively at the 5'-end by a phosphoramidate bond, allowing
immobilization of
more than 1 pmol of DNA (Rasmussen et al., (1991) Anal. Biochem. 198(1) 138-
42).
The use of CovaLink NH strips for covalent binding of DNA molecules at the 5'-
end
has been described (Rasmussen et al., (1991). In this technology, a
phosphoramidate bond is
employed (Chu et al., (1983) Nucleic Acids Res. 11(8) 6513-29). This is
beneficial as
immobilization using only a single covalent bond is preferred. The
phosphoramidate bond joins
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the DNA to the CovaLink NH secondary amino groups that are positioned at the
end of spacer
arms covalently grafted onto the polystyrene surface through a 2 nm long
spacer arm. To link
an oligonucleotide to CovaLinlc NH via an phosphoramidate bond, the
oligonucleotide terminus
must have a 5'-end phosphate group. It is, perhaps, even possible for biotin
to be covalently
bound to CovaLink and then streptavidin used to bind the probes.
More specifically, the linkage method includes dissolving DNA in water (7.5
ngl~l) and
denaturing for 10 min. at 95°C and cooling on ice for 10 min. Ice-cold
0.1 M 1-
methylimidazole, pH 7.0 (1-MeIm~), is then added to a final concentration of
10 mM 1-Melm~.
A ss DNA solution is then dispensed into CovaLink NH strips (75 ~1/well)
standing on ice.
Carbodiimide 0.2 M 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC),
dissolved in 10 mM 1-MeIm~, is made fresh and 25 pl added per well. The strips
are incubated
for 5 hours at 50°C. After incubation the strips are washed using,
e.g., Nunc-Immuno Wash;
first the wells are washed 3 times, then they are soaked with washing solution
for 5 min., and
finally they are washed 3 times (where in the washing solution is 0.4 N NaOH,
0.25% SDS
heated to 50°C).
It is contemplated that a further suitable method for use with the present
invention is
that described in PCT Patent Application W~ 90/03382 (Southern ~ Maskos),
incorporated
herein by reference. This method of preparing an oligonucleotide bound to a
support involves
attaching a nucleoside 3'-reagent through the phosphate group by a covalent
phosphodiester link
to aliphatic hydroxyl groups carried by the support. The oligonucleotide is
then synthesized on
the supported nucleoside and protecting groups removed from the synthetic
oligonucleotide
chain under standard conditions that do not cleave the oligonucleotide from
the support.
Suitable reagents include nucleoside phosphoramidite and nucleoside hydrogen
phosphorate.
An on-chip strategy for the preparation of DNA probe for the preparation of
DNA probe
arrays may be employed. For example, addressable laser-activated
photodeprotection may be
employed in the chemical synthesis of oligonucleotides directly on a glass
surface, as described
by Fodor et cd. (1991) Science 251 (4995), 767-73, incorporated herein by
reference. Probes
may also be immobilized on nylon supports as described by Van Ness et cxl.
(1991) Nucleic
Acids Res., 19(12) 3345-50; or linked to Teflon using the method of Duncan ~z
Cavalier (1988)
Anal. Biochem. 169(1), 104-8; all references being specifically incorporated
herein.
To link an oligonucleotide to a nylon support, as described by Van Ness et al.
(1991),
requires activation of the nylon surface via alkylation and selective
activation of the 5'-amine of
oligonucleotides with cyanuric chloride.
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One particular way to prepare support bound oligonucleotides is to utilize the
light-generated synthesis described by Pease et al., (1994) Proc. Nat'l. Acad.
Sci., USA 91 (11),
5022-6, incorporated herein~by reference). These authors used current
photolithographic
techniques to generate arrays of immobilized oligonucleotide probes (DNA
chips). These
methods, in which light is used to direct the synthesis of oligonucleotide
probes in high-density,
miniaturized arrays, utilize photolabile 5'-protected N aryl-deoxynucleoside
phosphoramidites,
surface linker chemistry and versatile combinatorial synthesis strategies. A
matrix of 256
spatially defined oligonucleotide probes may be generated in this manner.
4.21 PREPARATION OF NUCLEIC ACID FRAGMENTS
The nucleic acids may be obtained from any appropriate source, such as cDNAs,
genomic DNA, chromosomal DNA, microdissected chromosome bands, cosmid or YAC
inserts, and RNA, including mRNA without any amplification steps. For example,
Sambrook
et al. (1989) describes three protocols for the isolation of high molecular
weight DNA from
mammalian cells (p. 9.14-9.23).
DNA fragments may be prepared as clones in TvIl3, plasmid or lambda vectors
and/or
prepared directly from genomic DNA or cDNA by PCR or other amplification
methods.
Samples may be prepared or dispensed in multiwcll plates. About 100-1000 ng of
DNA
samples may be prepared in 2-500 ml of final volume.
The nucleic acids would then be fragmented by any of the methods known to
those of
skill in the art including, for example, using restriction enzymes as
described at 9.24-9.28 of
Sambrook et al. (1989), shearing by ultrasound and NaOFI treatment.
Low pressure shearing is also appropriate, as described by Schriefer et al.
(1990)
Nucleic Acids Res. 18(24), 7455-6, incorporated herein by reference). In this
method, DNA
samples are passed through a small French pressure cell at a variety of low to
intermediate
pressures. A lever device allows controlled application of low to intermediate
pressures to the
cell. The results of these studies indicate that low-pressure shearing is a
useful alternative to
sonic and enzymatic DNA fragmentation methods.
One particularly suitable way for fragmenting DNA is contemplated to be that
using the
two base recognition endonuclease, CviJI, described by Fitzgerald et al.
(1992) Nucleic Acids
Res. 20(14) 3753-62. These authors described an approach for the rapid
fragmentation and
fractionation of DNA into particular sizes that they contemplated to be
suitable for shotgun
cloning and sequencing.
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The restriction endonuclease CviJI normally cleaves the recognition sequence
PuGCPy
between the G and C to leave blunt ends. Atypical reaction conditions, which
alter the
specificity of this enzyme (CviJI**), yield a quasi-random distribution of DNA
fragments form
the small molecule pUCl9 (2688 base pairs). Fitzgerald et al.
(1992),quantitatively evaluated
the randomness of this fragmentation strategy, using a CviJI** digest of pUCl9
that was size
fractionated by a rapid gel filtration method and directly ligated, without
end repair, to a lac Z
minus M13 cloning vector. Sequence analysis of 76 clones showed that CviJI**
restricts
pyGCPy and PuGCPu, in addition to PuGCPy sites, and that new sequence data is
accumulated
at a rate consistent with random fragmentation.
As reported in the literature, advantages of this approach compared to
sonication and
agarose gel fractionation include: smaller amounts of DNA are required (0.2-
0.5 pg instead of
2-5 p,g); and fewer steps are involved (no preligation, end repair, chemical
extraction, or
agarose gel electrophoresis and elution are needed).
Irrespective of the manner in which the nucleic acid fragments are obtained or
prepared,
it is important to denature the DNA to give single stranded pieces available
for hybridization.
This is achieved by incubating the DNA solution for 2-5 minutes at 80-
90°C. The solution is
then cooled quickly to 2°C to prevent renaturation of the DNA fragments
before they are
contacted with the chip. Phosphate groups must also be removed from genomic
DNA by
methods known in the art.
4.22 PPA~A'~°ION ~F IDNA ~S
Arrays may be prepared by spotting DNA samples on a support such as a nylon
membrane. Spotting may be performed by using arrays of metal pins (the
positions of which
correspond to an array of wells in a microtiter plate) to repeated by transfer
of about 20 nl of a
DNA solution to a nylon membrane. By offset printing, a density of dots higher
than the density
of the wells is achieved. One to 25 dots may be accommodated in 1 mm2,
depending on the
type of label used. By avoiding spotting in some preselected number of rows
and columns,
separate subsets (subarrays) may be formed. Samples in one subarray may be the
same genomic
segment of DNA (or the same gene) from different individuals, or may be
different, overlapped
genomic clones. Each of the subarrays may represent replica spotting of the
same samples. In
one example, a selected gene segment may be amplified from 64 patients. For
each patient, the
amplified gene segment may be in one 96-well plate (all 96 wells containing
the same sample).
A plate for each of the 64 patients is prepared. By using a 96-pin device, all
samples may be
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spotted on one 8 x 12 cm membrane. Subarrays may contain 64 samples, one from
each patient.
Where the 96 subarrays are identical, the dot span may be 1 mm2 and there may
be a 1 mm
space between subarrays.
Another approach is to use membranes or plates (available from NUNC,
Naperville,
Illinois) which may be partitioned by physical spacers e.g. a plastic grid
molded over the
membrane, the grid being similar to the sort of membrane applied to the bottom
of multiwell
plates, or hydrophobic strips. A fixed physical spacer is not preferred for
imaging by exposure
to flat phosphor-storage screens or x-ray films.
The present invention is illustrated in the following examples. Upon
consideration of
the present disclosure, one of skill in the art will appreciate that many
other embodiments and
variations may be made in the scope of the present invention. Accordingly, it
is intended that
the broader aspects of the present invention not be limited to the disclosure
of the following
examples. The present invention is not to be limited in scope by the
exemplified embodiments
which are intended as illustrations of single aspects of the invention, and
compositions and
methods which are functionally equivalent are within the scope of the
invention. Indeed,
numerous modifications and variations in the practice of the invention are
expected to occur to
those skilled in the art upon consideration of the present preferred
embodiments. Consequently,
the only limitations which should be placed upon the scope of the invention
are those which
appear in the appended claims.
All references cited within the body of the instant specification are hereby
incorporated
by reference in their entirety.
5.0 E~~LE~"
5.1 E LE 1
Novel Nucleic Acid Seguences Obtained From Various Libraries
A plurality of novel nucleic acids were obtained from cDNA libraries prepared
from
various human tissues and in some cases isolated from a genomic library
derived from human
chromosome using standard PCR, SBIi sequence signature analysis and Banger
sequencing
techniques. The inserts of the library were amplified with PCR using primers
specific for the
vector sequences which flank the inserts. Clones from cDNA libraries were
spotted on nylon
membrane filters and screened with oligonucleotide probes (e.g., 7-mers) to
obtain signature
sequences. The clones were clustered into groups of similar or identical
sequences.
Representative clones were selected for sequencing.
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In some cases, the 5' sequence of the amplified inserts was then deduced using
a typical
Sanger sequencing protocol. PCR products were purified and subjected to
fluorescent dye
terminator cycle sequencing. Single pass gel sequencing was done using a 377
Applied
Biosystems (ABI) sequencer to obtain the novel nucleic acid sequences.
5.2 EXAMPLE 2
Assemblage of Novel Nucleic Acids
The contigs or nucleic acids of the present invention, designated as SEQ ID
NO: 1369-
1966 were assembled using an EST sequence as a seed. Then a recursive
algorithm was used to
extend the seed EST into an extended assemblage, by pulling additional
sequences from
different databases (i.e., Hyseq's database containing EST sequences, dbEST,
gb pri, and
LTniGene, and exons from public domain genomic sequences predicated by
GenScan) that
belong to this assemblage. The algorithm terminated when there were no
additional sequences
from the above databases that would extend the assemblage. Further, inclusion
of component
sequences into the assemblage was based on a BLASTN hit to the extending
assemblage with
BLAST score greater than 300 and percent identity greater than 95~/0.
Table 7 sets forth the novel predicted polypeptides (including proteins), SEA
~ NO:
1967-2564, encoded by the novel polynucleotides (SEQ ID NO: 1369-1966) of the
present
invention, and their corresponding translation start and stop nucleotide
locations to each of SEA
ID NO: 1369-1966. Table 7 also indicates the method by which the polypeptide
was predicted.
Method A refers to a polypeptide obtained by using a software program called
FAST'
(available from http://fasta.bioch.vir~inia.edu) which selects a polypeptidc
based on a
comparison of the translated novel polynucleotide to l~nown polynucleotides
('6~3.R. Pearson,
Methods in Enzymology, 183:63-98 (1990), herein incorporated by reference).
Method B
refers to a polypeptide obtained by using a software program called GenScan
for
human/vertebrate sequences (available from Stanford University, Office of
Technology
Licensing) that predicts the polypeptide based on a probabilistic model of
gene
structure/compositional properties (C. Burge and S. Karlin, J. Mol. Biol.,
268:78-94 (1997),
incorporated herein by reference). Method C refers to a polypeptide obtained
by using a Hyseq
proprietary software program that translates the novel polynucleotide and its
complementary
strand into six possible amino acid sequences (forward and reverse frames) and
chooses the
polypeptide with the longest open reading frame.
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5.3 EXAMPLE 3
111
Novel Nucleic Acids
The novel nucleic acids of the present invention were assembled from sequences
that
were obtained from a cDNA library by methods described in Example 1 above, and
in some
cases sequences obtained from one or more public databases. The nucleic acids
were
assembled using an EST sequence as a seed. Then a recursive algorithm was used
to extend the
seed EST into an extended assemblage, by pulling additional sequences from
different
databases (Hyseq's database containing EST sequences, dbEST, gb pri, and
UniGene) that
belong to this assemblage. The algorithm terminated when there was no
additional sequences
from the above databases that would extend the assemblage. Inclusion of
component sequences
into the assemblage was based on a BLASTN hit to the extending assemblage with
BLAST
score greater than 300 and percent identity greater than 95%.
Using PHRAP (TJniv. of Washington) or CAP4 (Paracel), a full-length gene cDNA
sequence and its corresponding protein sequence were generated from the
assemblage. Any
frame shifts and incorrect stop codons were corrected by hand editing. During
editing, the
sequences were checked using FAST Y and/or BLAST against Genebank (i.e.,
dbEST, gb pri,
UniGene, and Genpept) and the Geneseq (Dervvent). Other computer programs
which may
have been used in the editing process were phredPhrap and Conned (University
of Washington)
and ed-ready, ed-ext and cg-zip-2 (Hyseq, Inc.). The full-length nucleotide
and amino acid
sequences, including splice variants resulting from these procedures are shown
in the Sequence
Listing as SEQ ff~ NO: 1-1368.
The nucleic acid sequences ofthe present invention were conftrmed to have at
least
one transmembrane domain using the TMpred program
(htta://www.ch.embnet.or~/software/TMPRED form html). One of skill in the art
will
recognize that the proteins of the present invention may be utilized as either
a membrane-
bound target or a soluble protein.
Table 1 shows the various tissue sources of SEQ ID NO: 1-684.
The homologs for polypeptides SEQ TD NO: 685-1368 that correspond to
nucleotide
sequences SEQ ID NO: 1-684 were obtained by a BLASTP version 2.Oa1 19MP-WashU
searches against Genpept and Geneseq (Derwent) using BLAST algorithm. The
results
showing homologues for SEQ ID NO: 685-1368 are shown in Tables 2A and 2B.
Using eMatrix software package (Stanford University, Stanford, CA) (Wu et al.,
J.
Comp. Biol., Vol. 6, 219-235 (1999), httb://motif.stanford.edu/ematrix-search/
herein
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incorporated by reference), all the polypeptide sequences were examined to
determine
whether they had identifiable signature regions. Scoring matrices of the
eMatrix software
package are derived from the BLOCKS, PRINTS, PFAM, PRODOM, and DOMO
databases. Tables 3A and 3B show the accession number of the homologous
eMatrix
signature found in the indicated polypeptide sequence, its description, and
the results
obtained which include accession number subtype; raw score; p-value; and the
position of
signature in amino acid sequence.
Using the Pfam software program (Sonnhammer et al., Nucleic Acids Res., Vol.
26(1) pp. 320-322 (1998) herein incorporated by reference) all the polypeptide
sequences
were examined for domains with homology to certain peptide domains. Tables 4A
and 4B
show the name of the Pfam model found, the description, the e-value and the
Pfam score for
the identified model within the sequence. Further description of the Pfam
models can be
found at http://pfam.wustl.edu/.
Table 5 shows the position of the signal peptide in each of the polypeptides
and the
maximum score and mean score associated with that signal peptide using Neural
Network
SignalP V 1.1 program (fiom Center for Biological Sequence Analysis, The
Technical
University of Denmark). The process for identifying prokaryotic and eukaryotic
signal
peptides and their cleavage sites arc also disclosed by Henrik Nielson, Jacob
Engelbrecht,
Soren Brunak, and Gunnar von Heijne in the publication " IdentiEcation of
prokaryotic and
eukaryotic signal peptides and prediction of their cleavage sites" Protein
Engineering, Vol.
10, no. 1, pp. 1-6 (1997), incorporated herein by reference. A maximum S score
and a mean
S score, as described in the Nielson et al reference, was obtained for the
polypeptidc
sequences.
Table 6 correlates nucleotide sequences of the invention to a specific
chromosomal
location when assignable.
Table 8 shows the number of transmembrane regions, their location(s), and
TMPred
score obtained, for each of the SEQ ID NO: 685-1368 that had a TMPred score of
500 or
greater, using the TMpred program
(http:l/www.ch.embnet.or~/software/TMPRED form.html).
Table 9 is a correlation table of the novel polynucleotide sequences SEQ ID
NO: 1-
684, their corresponding polypeptide sequences SEQ ID NO: 685-1368, their
corresponding
priority contig nucleotide sequences SEQ ID NO: 1369-1966, their corresponding
priority
contig polypeptide sequences SEQ ID NO: 1967-2564, and the US serial number of
the
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113
priority application (all of which are herein incorporated in their entirety),
in which the
contig sequence was filed.
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114
TABLE 1
Tissue Ori Librar /RNA HYSEQ Librar SEQ ID NOS:
in Source Name
adult brain GIBCO AB3001 39-40 56 68
93
154-155 189
205
215 221 229
245
289-290 296
298
305 307 314
324
346 362 376
384
438 444 493
499
502 532 563
612
624 654 668
adult brain GIBCO ABD003 10 13 15 17-20
27
29 34 40 47-49
56
61-63 66 68
75 80-
82 86 93-94
96 98
102 106 137
150
154 156-159
161
168-169 173-174
179 188 205
210
212 215 221
229-
231 243 245
290
296 302 305
307
313-315 319-320
323 325 331
346
349 352 359
362
367 371 376
384
420-421 428
438
444 447 461-462
473-474 487
493
499 516 519
522-
523 529 532
541
550 563 587-588
601 612 616
624
627 635 643
652-
654 660 669
672-
673 677-678
adult brain Clontech ABR001 7 18 22 24 29
47-
50 56 68 70
75 79
112-113 152
161
186 205-206
212
220 230 259-262
280 282 296
302
346 361 376
384
420 465 488-489
492 518 520
587
595 620-621
652
660 682
adult brain Clontech ABR006 7-8 10 13 16
20-21
23 27 34 37
40 53
56 64-65 69-70
73-
74 79 88-89
92 100
104-105 147-150
160-161 170
186
200 207 212
229-
230 243 256
259-
262 266 275-278
280 282-283
287
289-290 307
309
314-315 317-318
321-322 325
337-
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115
TA13T,F 1
Tissue Ori Librar /RNA HYSEQ Librar SEQ ID NOS:
in Source Name
338 349-352 357
359-360 364 377
384 430 447-448
461 466 484 499
501 503 518 520
530 532 542-546
552 556 562-563
569-571 600 607-
616 620-621 623-
625 628-629 641-
642 653 660 672-
673 677-678 682
adult brain Clontech ABR008 7-8 10 14 19 21
23
25-28 30-33 37-39
43 46-50 52-53
56-
57 59 62-65 67-68
73-76 86-89 92-94
104-105 118 131-
l34 139-140 144
147-148 150 153-
154160-165 170
180 186 189 205-
206 208-212 218-
219 223 229-230
232-234 236 242-
245 249 259-263
266 268 270 273
283-289 293 298
302 305 307-308
313-316 318-324
334-335 337-341
343 346 349 35l
356 359 361-364
367 371 377 381
384 387-388 390
403-404 419 423-
425 431 435-436
438 440-441 445-
451 462 473-475
484 493 498-501
504-506 509 512
514-522 525 527
529-530 S32 534
543-545 550 558
562-564 569 576
583-584 591 597-
599 601-602 605
607-610 620-621
624-625 627-628
631-632 638-640
652-653 660 663
665 670-671
adult brain Clontech ABRO11 289 384 537
adult brain BioChain ABR012 26 384 607
adult brain BioChain ABR013 20 79 153 220
289
384 465 526
adult brain Invitrogen ABR014 48-50 52 106 170
230 335 384 430
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TABLE 1
Tissue Ori Librar /RNA HYSEQ Librar SEQ ID NOS:
in Source Name
438 501 530 536
635 643
adult brain Invitrogen ABR015 20 46 106 150
l53
216 371 384 401
461 526 643
adult brain Invitrogen ABR016 60 69 153 368
384-
385 507 522 587
654
adult brain Invitrogen ABT004 10 16 24 29 43
47-
49 56 60 64 67-69
73 79 97-98 165
168-170 179 186
189 205 230 242-
247 249 259-263
289-290 296 298
305 308-310 314-
315 319 329-330
332-333 349 359
380 384-385 387-
388 390 428 451
456-457 475 487-
490 492-493 499-
500 512 519-520
522 529-530 587
612 620-621 643
654 663 665
cultured Stratagene ADP001 10 19-20 23 26
36
preadipocytes 68 70 106 116-117
147-148 165 171-
172 189 220 246-
247 256 273 289
305 316-319 329-
330 349 35l 361
365 392 394-398
400 423-424 428
451 465 487 499
507 522 529 534
543 587 643 672-
673 682
adrenal glandClontech ADR002 10 18 25 27 29
47-
49 52-53 56 64
73-
75 83 87 90 100
106 110 124 130
137 144 160-161
163 182 189 198
200 202-203 208
211-212 215 217
220 237-241 249
251 259-263 280
289-293 296 317-
319 329-331 344-
345 359 362 371
377 384 390 403-
404 423-424 426
465 499-501 507
516 522 525 539
570 572-573 585
600-601 611 620-
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117
TABLE 1
Tissue Ori Librar /RNA I3YSEQ Libra SEQ ID NOS:
in Source Name
621 623-624 635
643 660 663 672-
673 675
adult heart GIBCO AHR001 5 16 18 24-26
34
37 39 46 56 64
66-
68 75 77 83 86-89
92 94-97 101-102
104-106 110 134
150 154 158-l59
162 168-170 194-
196 202-203 212
215 224-226 229
269 289 296 302
306 308-309 314
320 323-324 331
336-338 342 346
356 367 371 377-
378 384-385 390
400 402 417-418
421 428 431 436
438 447 461-462
475 479 484-485
491 498 501 507
516 518 522-525
530 532 534 541
554 564 570 572-
573 586-587 60l
605 607 610 613-
614 635 643 652
662 669 672-673
adult kidney GIBCO AKD001 5 10 12-13 16
18
20 24-26 29 39
43
52 54 56 62-64
66
68 71-72 75-76
83
89-96 98 106-109
112-114 116-117
122-126 131 137
139 155 158-159
162 170 172-174
177 183-184 188
200 202-203 205
208 215-216 218-
219 229-230 245
247 256 268 272
275-278 289-290
296 298-299 302
308-309 314 316
319-320 323 329-
330 332-333 336
350 359-360 364
367-368 371 377
384 392-393 400
402 420 423-424
428 431 435-436
438 444 451 461
473-474 484-486
492-493 499-500
504-507 510 516
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118
TABLE 1
Tissue Ori Librar /RNA HYSEQ Libra NameSEQ ID NOS:
in Source
518-519 52l-522
524 526 529-530
532 534 537 539
541 567-568 587-
588 613 620-621
623 631-632 635
643 652 654 664
668 672-673
adult kidney Invitrogen AKT002 6 8 10 14-15
17 20
24-25 29 33-34
40
46-50 64 67 75
80-
82 85 88 93-94
106
116-117 l26 150
154 157 162-164
168-169 188 199
216-219 222 232-
234 255-256 271
275-278 289 296
298 308 312 317-
319 332-333 337-
338 348 358 360
368 370-371 384
390 400 421 430
435 438 451 461-
462 491-493 499-
501 507 509 516
518 520 522 524
530 535-537 552
564 567-568 580
587 597-599 607
631-632 635 643
652 662 666 669
672-673 675 677-
679
adult lung GIBCO AhG001 13 22 26 63 66
68
75 93 106 112-114
127-130 137 144
150 165 177 230
256 271 289 302
314 323 327 337
342-343 368 371
384 390 392-393
421 484 488-489
504-507 539 564
638-639 643 661
675
lymph node Clontech ALN001 13 26 33 54 56
128-131 135 150
166 173-174 202-
203 211 215-216
256 259-262 289
320 327 350 367-
368 371 465 507
509 526 643 669
young liver GIBCO ALV001 5 10 13 24-25
43-
44 56 67-68 71
80-
82 89 106 110-111
132-133 137 154
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119
TABLE 1
Tissue OriginLibrar /RNA ~HS'SEQ Library SEQ ID_ NOS:
Source Name
168-170 179 183-
184 205 218-219
221 229 275-278
296 302 320 367
371 390 428 438
487-490 498 502
507 525 530 538
635 641-643 651
666
adult liver Invitrogen ALV002 5 14 16-17 19
24-
25 37 52 64 66
68
80-82 87 90 93
97-
98 104-105 132-133
137 140 150 170
183 186 188 215
218-220 229 232-
234 249 256 272
275-278 289 294-
295 311-312 314
319 332-333 351
358-359 364 366
371 377 381 386-
387 392-393 428
449 451 465 487-
489 495-498 518
522 538 593 601
607 610 631-632
643 666
adult liver Clontech ALV003 7 18-19 24 38
46
180 186 216 220
222 249 275-278
371 390 427 465
495 499 530 538
623 627 632 666
679-680
adult ~vary~ Invitrogen AOV001 5 7-8 10 12 14
16
18 20 25-27 29
33
36 38-40 47-49
53-
54 56 59 61-62
64
67-68 73-76 79-83
87 89 92-94 96
98
106-107 111-114
116-118 121 128-
131 134-135 137
139-142 150 153-
154 157-l61 171-
177 179-180 182
187 189 194-198
200 202-203 205-
206 211 218-219
222 229-230 235-
241 245 249 251
254-256 259-264
267 272 282 289-
290 296 298-299
302 305-306 308
311-314 316 320
323-325 327 331-
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TABLE 1
Tissue Ori Librai '/RNA HYSEQ Librar SEQ ID NOS:
in Source ~ Name
333 336 342 346-
347 349-351 358
362 367-368 371
377 380 383-384
390 392-393 400
402 420-423 425
427-428 435-436
438 444 451 454
459-462 471 473-
474 484 487-489
491 493 498-499
501-502 504-507
511 516 518 521-
522 524 530 532
539 543 547-550
555-556 564-565
581 587 593 595
602 605 607 616
620-621 623-624
631-632 635 643
652-654 660 667-
669 679-680
adult placentaClontech APL001 1-4 63-64 66
143
145-146 178 211
216 289 296 323
351 384 537 630
placenta , Invitrogen APL002 1-4 7 51 68 85
98
151-152 192 208
215 256 259-262
305 319 332-333
384 428 499 533
602 627 654 666
adult spleen GIBCO ASP001 7 13-14 17 26
32
52 54 56 63 75
89
106 109 112-115
l20 135 137 141-
142 144 154 157
173-174 179-180
186 205 208 216
220-222 229 252
256 259-262 272
279 289 296 298
302 308 312 319-
320 337-338 347
364 367-368 371
384 400 427 438
451 459-461 465
484 487 500 504-
507 522 525-526
530 534 555 587
593 617-618 631-
633 635 638-639
643 663 669 675-
676 679
adult testis GIBCO ATS001 5 10 19 29 39
64
68 93 100 106
ll6-
117 137 145-146
150 153 172 l75-
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121
TABLE 1
Tissue OriginLibrary/RNA IiYSEQ Librar SEQ ID NOS:
Source Name
176 181-182 198
202-203 229 249
256 267 289 296
298 302 305 307-
308 314 316 323
331 356 359 362
364 371 384 402
426 438 451 485
500 507 518-519
591 597-599 619-
621 643 654 662
adult bladderInvitrogen BLD001 5 10 26 51 65
68
84 89 93 131
175-
176 211 256 259-
262 267 289 314
317-318 332-333
351 383-384 395-
398 423-424 426
499 501 522 525
580 593 643 661
682
bone marrow Clontech BMD001 5 7 30-31 34
37 40
47-49 54-56 62
68
75-80 83 93 96
100
131 136 147-148
150 158-159 163
165 172 l77 198
204 206 211 216
229 289 302 308
316 319-320 324-
325 337-338 350
358 364 367-368
371 400 422 428
438 452 454 461
478 484 487 491
499-502 507 509-
510 520 530 536-
537 541 543 554
587 624 638-639
643 651-652 654
667-669 672-673
bone marrow GF BMD002 7-8 12 14 17
20 25
27-28 32-33 37
43
52 57 63-64 66-68
77 87 100 102
106-
107 112-114 116-
118 120 131 136-
137 144 147-148
150-153 157-159
163 172 179 199
206 215-216 222
256 259-263 268
272 275-278 286
289 298 302-303
305 308 317-318
325 337-338 341
343 347-348 368
371 390 400 427-
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122
TABLE 1
Tissue Ori Librar /RNA HYSEQ Librar SEQ ID NOS:
in Source Name
428 430-431
434-
435 437 444
451
461-462 488-489
491-.492 499
501-
502 504-507
509
511 516 520
525-
526 530 537
543
554 558 560-561
585 587 595
600
610 623 629
631-
633 635 638-640
643 667-669
672-
673 679
bone marrow Clontech BMD004 507 522
bone marrow Clontech BMD007 368 504-506
672
*Mixture of Various VendorsCGd010 99 132-133 165
16
tissues - 237-241 275-278
mRNA
290 298 306
336
368 380 402
423-
424 509 556
586
610
*Mixture of Various VendorsCGd011 33 42 153 168-169
16
tissues - 178 213-214
mRNA 245
247 467 526
537
572-573 675
Mixture of Various VendorsCGd012 5 14 18 21 24
16 31
tissues - 33 35 39 42
mRNA 44 46
51 53 58 61-62
70-
72 75 80 84-85
90
92-93 96 98
100-
103 127 131
144-
146 153-154
157
160-161 163
165
168-169 175-176
178-179 183
185
189 193 200
218-
219 221 229
232-
234 245 247
256
259-262 275-278
280 289-292
298
300-301 308
311
317-318 325
335-
338 342 344-347
349 352 355-356
359-360 368
370-
375 380 384-386
388 391 394-399
401-402 405-407
410 412-413
419
428 450-451
464
467-469 471
504-
507 512 516
518
524 526 532
537
541 545 547-549
554 556 563-564
572-573 586
590-
591 600 602
605
623-625 627-628
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123
TABLE l
Tissue Ori Librar /RNA IiYSEQ Librar SE ID NOS:
in Source Name
652 654 659-660
664 667 670-671
676 682
*Mixture of Various VendorsCGd013 56 58 61-62 70
l6 131
tissues - 160-161 163-l64
mRNA
193 247 290 31l
345 348 360 368
370 394-398 512
537 556 660 682
*Mixture of Various VendorsCGd015 1-5 8 14 17 52
16 59
tissues - 68 87 215 228
mRNA 259-
262 272 275-278
289 309 371 377
392-393 400 402
420 446-447 451
492 498 504-506
514 521 537-538
588 620-621 637
643 654 672-675
*Mixture of Various VendorsCGdOl6 10 14 19 24-28
l6 33
tissues - 57 65 70 76 112-
mRNA
114 121 131 151-
153 163 183 206
218-219 325 328
332-333 394-398
435 440-441 488-
489 500 510 518-
520 532 569 590
641-643 653 662-
663 668 671-673
682
adult colon Invitrogen CLN001 5 10 14 29 35
47-
50 56 112-114
135
175-176 179 220
230 254 256 289-
290 308 332-333
343 368 371 385-
386 415 427-428
436 465 498 510
518 534 572-573
580 597-599 607
643 651 661 663
669
adult cervix BioChain CVX001 7 10 14 16 18
20
23-26 30-31 40
47-
49 56 62 66 70
73-
76 83 85 87 89
93-
94 97 103 106
126
131 137 141-142
144 147-148 154
175 177 179 182
188-189 197-198
202-203 206 211
221 229 245 249
259-263 267 282
287 289 296 298
302 305 308 314
320 323-325 329-
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124
TABLE 1
Tissue Ori Library/RNA Iii'SEQ Librar SEQ ID NOS:
in Source Name
333 350 356
358
362 367-368
371
377 382 384
390
400 438 451
454
459-460 462
465
484 487-490
492-
493 499-502
507
516 522 524-525
530 532 534-535
541 550 555
572-
573 580 587
602
605 610 613-614
616 623-624
626
628 643 652
661
663-664 668
680
682
diaphragm BioChain DIA002 93 l34 308 402
endothelial Stratagene EDT001 7 10 12 17 19
23
cells 29 34 36 39
52 54
56 63-64 66
68 75
80-84 86-89
92-93
95-97 106-107
116-
117 127 l31
137
139 147-148
150
154 157-159
168-
169 172 179
182
192 198-199
202-
203 208 211
215
217 220-221
230-
234 249 254
256
259-262 264
270
272 289-290
296
298 313-314
316
320 323-324
348-
350 364 367
371
376-377 390
392
430 435 438
445-
446 465 473-475
484 487-489
492
498-499 502
504-
507 510 5l8
522
524 532 541
543
552 554-555
587-
588 595 602
610
631-632 643
651-
654 662 668-669
672-673
fetal brain Clontech FBR001 8 24 54 56 59
69
88 229 384 428
440-441 541
628
671
fetal brain Clontech FBR004 20 53 160-l61
170
293 385 461
530
605 620-621
654
660
fetal brain Clontech FBR006 7-8 10 15 18-19
24-26 29 33
46 53
56 59 62-64
66 68
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125
TABLE 1
Tissue Ori Librar /RNA NYSE Librar SEQ ID NOS:
in Source Name
70 73 79 84 87
131
140.147-l48 155
163 l65 170 179-
l80 189-190 208
211 218-219 229-
230 232-234 236
245 249 259-262
267 284-287 293
298 305 308 313-
314 316-319 322
324 337-338 343-
346 350-351 354
359-362 376 380-
381 384 387-398
403-404 423-424
428 431 435 438
440-441 445-447
451 462 473-475
484 492 498-501
504-507 509 512
516 518-519 521-
522 529-530 532
541 543 550 554
558 566 568-570
576 591 597-599
603 605 607-609
623-625 627-632
640 643 652-653
662-663 665 667
671-673 675 682
fetal brain Clontech FBRs03 17 371
fetal brain Invitrogen FBT002 7 10 29 43 47-49
52 60 64-65 67-68
79 83 86 92 94
131
139-140 168-169
180 202-203 205
218-219 230 242-
243 259-262 289
296 298 302 305
307 319 329-330
332-333 364 380
390 392-393 451
473-474 484 492
499-500 518 520
537 553 607 619
643 654
fetal heart Invitrogen FHR001 8 14-15 20 24-26
34 37 39 46 53
56-
57 60 63 70 75
80-
82 96-98 101 106
120 127 131 134
153 161 168-169
171 180 202-203
216 229 236 266-
267 289-290 303
305 308 314 316
325 344-345 356
358-359 363 366
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126
TABLE 1
Tissue Ori Library/RNA HYSEQ Librar SEQ ID NOS:
in Source Name
371 384 392-393
395-398 400 402
419 422 431 434
436 438 451 453
461-462 478 484
500 504-506 518
522 525-526 530
535 537 539 541
550 570-573 586-
588 590-591 597
601 605 610 613-
614 626 630-632
640 643 652 669
672-673 675 682
fetal kidney Clontech FKD001 26 62 96 106
115
150 153 217-219
259-262 289 308
323-324 350 371
428 435 507 522
537 643
fetal kidney Clontech FKD002 46 54 64 68 85
107-108 126 131
155 158-159 163-
164 167-169 188
224-226 229 232-
234 236 245 282
284-285 289-290
293 298 340-341
343 350 370 417-
418 431 436 438
461 484 499-500
516 518 532 567-
568 572-574 589
596-599 613 624-
626 628 640 671-
673
fetal kidney Invitrogen FKD007 227
fetal lung Clontech FLG001 25 40 56 75 93
106
112-114 131 229
316 428 436 484
499 572-573 623
fetal lung Invitrogen FLG003 5 7 10 16 22
25-26
44 47-50 57 75
79
102 106 148 157
175-176 189 191
256 259-262 314
356 359 371 384
399-400 423-424
428 430 451 488-
490 500 504-507
518 529-530 534
539 550 556 620-
621
fetal lung Clontech FLG004 305
fetal liver- Columbia FLS001 1-5 7-8 10 12
14-
spleen University 17 19-20 24-27
29-
54 56-57 62-64
68
71 75 80-83 85
87-
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127
TABLE 1
Tissue Ori Librar /RNA HYSEQ Librar SEQ ID NOS:
in Source Name
97 99-100 104-107
109-110 131 137
141-142 150-153
l55 168-169 177-
180 183-184 188
198 200 202-203
205 208 212 215-
220 222 229 245
251-252 256-262
264 267 271-273
275-279 289-290
296 298 302 306
308 314 3l6-318
320 324-325 331-
333 337-338 349-
352 359 364 366-
368 371 377 383
386-387 390 392-
393 400-401 403-
404 420-421 423-
424 428 434-435
438 440-441 445-
446 451 455-457
459-462 475 479-
481 484 487 491-
492 498-507 510-
511 516 518 521-
524 526 530 533
536-538 541 543
550 554-556 558
588 593 595-598
601-602 605 607
610 613 620-621
623-624 629 634
641-643 651-652
667-668 671-673
675 681
fetal liver- Columbia FL5002 2-5 7-8 10 12
14-
spleen University 17 19 24 26-27
34
36 38 40-42 44
47-
49 52-54 56-57
62
64 66 68 71 75-76
80-83 85-86 88-89
91-93 96 98-100
106-108 110 112-
113 115-117 128-
131 135 137 139-
142 150 153 157-
159 163 171-174
179 183-184 186
188-189 192 198
200 202-203 206
208 212 216 218-
220 229-230 236-
241 245 249 252
256-262 275-279
290 294-295 298
302 305-306 308
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128
TABLE 1
Tissue Ori Librar /RNA I3YSEQ Libra SEQ ID NOS:
in Source Name
312-314 316-320
324-325 327 335
337-338 342 349-
350 357-360 366-
368 376-379 387
390 400 419-420
426 428 434 436
438 440-441 444
456-457 459-462
478 48l-482 486-
492 498-499 501
504-506 508-509
516 5l8 521-522
527 530 534 536-
537 543 554-555
564 581 587-588
595 597-598 601
605 610 613 620-
621 623-625 627
629 631-632 634
641-643 651-652
662 666-668 671-
673 675 683
fetal liver- Columbia FLS003 2-5 14 l8 20
24 26
spleen University 44 62 64 68 80-83
88 93 99-100
106
137 153 157 163
183 197 222 229
236 245 256 275-
278 289 298 306
315-318 331 337-
338 346 350 359
366 371 419-420
428 436 438 491-
492 502 507 518
521-522 530 538
543 555-556 593
623-624 652 667
672-673 679
fetal liver Invitrogen FLV001 5 10 24 46 52
64
67-68 157 168-169
180 202-203 211
216 218-219 222
237-241 256 259-
262 272 275-278
317-318 321 324
332-333 342 347
351 371 401 421
428 434 451 488-
490 498 593 623
643 679
fetal liver Clontech FLV002 10 24 140 153
l70
230 249 256 275-
278 284-285 325
358 366 392-393
500 518 538 576-
577 613 623 641-
642 666
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TABLE 1
Tissue Ori Librai /RNA HYSEQ Librar SEQ ID NOS:
in Source Name
fetal liver Clontech FLV004 5 13-14 18 20
24
35 46-50 56 63-64
68 75 100 102
106
108 116-118 137
140 144 147-148
170-172 2l8-219
236 256 259-262
275-278 318 323
325 329-330 340-
341 356-357 371
390 428 431 436
438 440-441 453
461-462 498-499
518 530 537-538
543 587-588 623
629 632 638-639
643 651-652 662
666 671-673
fetal muscle Invitrogen FM5001 5 16 24-26 64
93
139 144 168-169
171 175-176 181
202-203 212 218-
219 256 289-290
296 298 317-318
349 356 364 371
377 380 392-393
402-404 427 444
518 523 564 586
623 661-662
fetal muscle Invitrogen FMS002 6 15-l6 21 26
29
37 41 52 57 75
87
96 101-102 106
116-118 131 158-
l59 167-169 171
180 189 256-258
272 289-290 293
298 306 308 316
325 332-333 343
351 353 356 380
382 388 400 402
411 416 419 428-
429 431 453 499
516 522 525 530
532 541 543 550
563 565-568 572-
573 584 586 603
613 623 643 662-
663
fetal skin Invitrogen FSK001 5 7-8 10 14-17
20
23 25-26 29 36-37
39 41 46 51 53
68-
70 80-82 84 86
90
92-93 96 111
127-
130 132-133 141-
142 147-148 151-
152 158-161 163-
165 173-174 202-
203 205-207 218-
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TABLE 1
Tissue Ori Librar /RNA HYSEQ Librar SEQ ID NOS:
in Source Name
220 224-226 229-
230 245 254 256-
262 289-290 296
298 302 305 308-
309 315-316 319
324-325 327 358-
359 364 369 371
388 392-393 400
405-413 417-418
436 438 440-441
451 458-465 467-
472 476 487 492
499 518-520 525
530-532 547-549
558 564 571 580
583 591 607 610
617-618 620-621
623 627 643 652
659-663 671-673
680 682
fetal skin Invitrogen FSK002 5 10 16 18 20
23-
26 36-37 39 41
46
52-53 56 61-65
68
70 80-83 87 94
96
100 130-131 148
158-159 162-164
168-169 182 188
193 201 220 224-
226 229 235-241
245 249 254 257-
262 289-290 293
298 302 316 318
325 331-333 335
340-341 350 359
361 363-364 371
390 392-398 400
403-404 408-409
41l 417-418 422
428 431 436 440-
441 451 453,.462
464-465 467 471
476 478 484 499
502 504-506 512
516 518 521-522
530 532 54l 543
547-549 556 564-
565 568 587 589-
591 593-594 597-
598 613-614 616
624-625 629 631-
632 637 640 643
652 662 667 669
671-673 681-682
fetal spleen BioChain FSP001 26 87 371 461
667
umbilical cordBioChain FUC001 5 18 20 26 40
47-
49 70 72 83 86-87
93 96 106 110-111
116-117 124 126-
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TABLE 1
Tissue Ori Librar /RNA I3YSEQ Librar SE ID NOS:
in Source Name
127 134 144 152-
153 155 157-159
161 165 171 182
206 218-219 224-
226 229 243 247
249 256 259-262
289 296 298 303
305-306 308 314
316 325 332-333
337-338 344-345
349 352 359 364
371 394-398 400
417-421 427 431
436 438 453 473-
474 477 479 499-
500 507 512 522
525 535 537 565
593 595 613 620-
621 623-624 637
643 653-654 660-
661 668-669 682
fetal brain GIBCO HFB001 5 10 18-21 27
34
38-40 47-49 52
56-
60 62 64 66-70
72-
76 80 83 86 92-93
134 139 141-142
149-150 155 170
172 179-180 185-
186 188 202-203
205 207 209-212
216 229-230 256
286-287 289 294-
296 298 314 319-
320 323 325 337-
338 346 350 357
367 371 376 381
384 420 436 438
444 447 454 459-
462 475 484 487
492-493 499-500
507 518-519 522
529-530 532 534
541 543 563 570-
571 580 597-598
601 607 616 619-
621 623-624 643
653-654 662 664
668 671-673 675
677-678 682
macrophage Invitrogen HMP001 18 26 43 64 118
144 179 211 245
329-330 347 371
427 435 461 502
530 537 620-621
635 638-639
infant brain Columbia IB2002 7 14 16-17 21
23
University 25-26 29 40 47-50
56-57 59-60 64
67-
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TABLE l
Tissue Ori Library/RNA HYSE Librar NameSEQ ID NOS:
in Source
68 70 73-74 79
83
88 91-92 94 98
103
115 127 137 139
150-152 156 158-
159 161-163 173-
174 182 186 188-
189 197 202-203
205-215 230 245
259-262 264 268
280 285 289 296
298 305 307-308
313-316 319 322-
324 326 334 346-
347 349-351 359
363-364 367 371
376-377 390 420
431 436 438 444
447-449 451 453
461-462 479 487
492 498-501 504-
506 516 519 522
529-530 537 541
543 545 556 564
572-573 588 592-
593 597-598 600
604-605 607 6l0
619 622 624 627-
628 643 652-654
660 663 674-675
682
infant brain Columbia IB2003 7 10 16 19-20
25
University 29 35 43 46-50
56-
57 59-60 64 68
70
79-82 87 92 106
139 150 158-159
162-163 165 173-
174 181 186 189
202-203 205 210-
214 229-230 245
256 259-263 289-
290 298 305 307-
308 314-315 319
322 328 334 337-
338 347 349 351
359 364 371 380
385 428 436 438
444 447 449 451
462 475 484 487
492-493 498-502
519 522 529-530
532 537 540 550
556 593 602-605
607 616 622 627
631-632 643 652-
654 663 672-673
682
infant brain Columbia IBM002 47-50 84 151-152
University 157 188-189 209
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TABLE 1
Tissue Ori Library/RNA HYSEQ Library SEQ ID NOS:
iu Source Name
289 390 423-424
453 628
infant brain Columbia IBS001 10 16 29 46-50
56
University 58 67 78 80-82
156
163 186 259-262
285 305 315
334
349 452 488-489
522 532 540
lung, Stratagene LFB001 5 7 16 19 40
54 56
fibroblast 61-62 68 83
93 106
116 121 137
172
191 198 205
223
256 289 325
329
349 371 400
438
484 501-502
507
518 522 525
532
541 610 631-632
643 651 669
lung tumor Invitrogen LGT002 5-7 10 15-16
18-l9
26 29 34-36
38 40-
41 46-50 52
56 59
64 68 75 86
89 91-
96 103-106 112-114
116-117 120
128-
130 135 141-142
144 147-148
150
154-155 157-159
162-164 172-174
179-180 190-192
198 202-203
208
215 220-221
223
229 236 249
255-
258 263 271
275-
278 284-285
291-
292 296 302
309
314 316 319
323
327 331 342
349-
351 353 358
364
368-369 371
390
392-393 399-400
420-421 427
431
436 438 444
453-
454 459-462
465
470 484 486
488-
492 499-500
502
507 511 518
522
525-526 530
537
539 543 550
580
597-599 605
623-
625 627 637
643
652 661-662
665-
666
lymphocytes ATCC LPC001 13 16 18 20
27 43
47-49 54 62-64
66-
68 80 87 90
96 98
115 118 120
131
144 163 202-203
211 252 256
259-
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TABLE 1
Tissue Ori Librar /RNA IiYSEQ Librar SEQ ID NOS:
in Source Name
262 265 290 296
308 324-325 347
350 358 371 377
384 400 420 428
436 462 467 470
483-487 499-502
504-507 509 518
522 525 530 543
545 550 588 600
605 607 624-625
633 635 643 645
654 669 672-673
675
leukocyte GIBCO hUC001 10 16 18 24 34
38-
40 43-44 47-50
52
54-57 62-64 66
68
78 80-82 86-89
93-
94 98 l06 109
111-
120 131 134 137
139 144 150-152
154 163 165 177
179 186 189 198
202-203 208 211
218-219 221 229
236 247 249 252
256 259-264 270
275-278 289-290
298 302 305 308
315 317-318 323
325 328 337-338
342 347 350 358
364 368 371 390
392-393 421 427-
428 430 433-435
437-438 440-441
444 451-452 454
461 475 484-487
491 493 498-500
502 504-507 509
518-519 522 525-
526 530 535 54l
543 550 555 586-
588 597-598 605
607 610 620-621
624 627 631-633
638-639 643 652
654 668-669 672-
673 675-676
leukocyte Clontech LUC003 20 47-49 52 56
100
112-114 198-199
314 337-338 348
371 438 484 502
530 537 602 633
643
melanoma from-Clontech MEL004 14 25 34 47-49
56
cell-line-ATCC- 64 66 83 92 106
#CRL-1424
111 131 134 137
l39 150 162 173-
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TABLE 1
Tissue Ori Librar /RNA IiYSEQ Librar SEQ ID NOS:
in Source Name
l74 189 192 210
229 249 259-262
290 321 337-338
350 364 371 392-
393 438 440-441
444 475 493 499
507 554 587 643
651 667 669 671
mammary glandInvitrogen MMG001 5 7 10 16-17
19 25
46-53 56 64 68
70
79-82 85-86 89
92-
95 98-100 106
121
127 137 139-142
l44 150-152 158-
159 161-164 180
189 192-193 198
202-203 205-206
216 218-220 230
245 249 252 259-
263 267 270-272
275-278 289-290
298 302 305 308
313 315 319 324
329-330 336 346
349 351 355-356
359 364 368 370-
371 377 384 390
392-393 421 425
427-428 436 444
451 455-460 462
465 473-474 487
492 499 502 507
516 518 524-526
-
529-530 533-534
539 543 583 590
592 602 605 613
623 627 63l-632
643 646 660 677-
678 682
induced neuron-Stratagene NTD001 17 20 23 68 79
89
cells 153 155 181-182
212 218-219 235
298 346 352 358
376 438 478 484
488-489 492-493
499-501 541 570
619 627 643 662
672-673
retinoic acid-5tratagene NTR001 7 23 56 68 70
131
induced- 186 189 213-214
neuronal-cells 290 293 342 461
499 504-506 530
601-602 607 682
neuronal cellsStratagene NTU001 7 29 42 68 70
84-
85 92 131 140
147-
148 202-203 259-
262 305 316 319
336 371 395-398
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TABLE 1
Tissue OriginLibrar /RNA IiYSEQ Librar SEQ ID NOS:
Source Name
461 493 499 502
537 550 553 592
652 672-673 682
pituitary Clontech PIT004 2-4 47-49 56
gland 68 72
93 l37-138 141-l42
150 154 158-159
177 182 192 221
229 272-273 290
298 308 316 325
329-331 342 346
356 360 436 459-
460 462 473-474
484 504-507 524
532 534 541 543
564 623 631-632
635 643 662
placenta Clontech PLA003 1-5 7 12 26 37
41
53 64 75 85 87
96
106-107 112-114
131 151-152 157
223 236 256-262
303 306 316 335
350-351 359 37l
400 428 431 435
438 445-446 462
499 502 516 520
530 532 537 543
550 556 565 579
587 594-595 626
635 638-639
prostate Clontech PRT001 20 25 56 173-174
205 250 256 280
284-285 299 302
309 320 323-324
331 342 349 362
367 384 386 392
400 415 438 484
498 507 524 532-
534 590 620-621
623 631-632 654
677-678 680
rectum Tnvitrogen REC001 7 10 20 47-50
52
85-87 89 109-110
126 128-130 157
163 170 173-174
177 205 220 229
256 259-262 289
319 324 327 340-
341 347 364 368
371 377 415-416
423-424 427 436
465 504-506 581-
582 602 610 679
salivary glandClontech SAL001 5 10 22 25 43
52
63-64 67 89 95
97
99 137 140 161
165
167-169 180 205
229 252 256 290
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TABLE 1
Tissue Ori Libra /RNA HYSEQ Librar SEQ ID NOS:
in Source Name
323 351 368 37l
430 436 438 487
502 507 516 525
564 580 613 617-
618 631-632
saliva gland Clontech SALs03 20
skin fibroblastATCC SFB001 208
skin fibroblastATCC SFB002 208
small intestineClontech SINOOl 5 7-8 10 15 24
26
37-38 47-49 51-54
56-57 59 64 67-68
72 75 88 93 96-97
l00 106 108 111
116-117 121 128-
131 137 140 153
158-159 177 189
191 202-203 206
215 229 253 255-
256 259-262 264-
265 272 280 296
300-301 308-309
316-318 325 327
332-333 335 337-
338 344-345 347
352 359 368 371
386 390 392-393
423 431 435 438
444 462 479 484
492 507 509 522
525-526 532 534
550 572-573 581
593 605 620-621
623 628 632 643
650 652-654 672-
673
skeletal muscleClontech SKM001 5 62 101 104
134
165 254 272 289
300-301 308 316
323 356 377 402
428 431 438 444
451 462 541 543
550 572-573 586
skeletal muscleClontech SKM002 208 507
spinal cord Clontech SPC001 13 15 26-27 33-34
38-40 46-50 52-53
56 68 80-82 87
89
92-95 131 150
155
163 175-176 180
186 197 199 202-
203 205 211 213-
214 229 231 235
254 263 289 307
311 314-316 323-
324 329 340-342
348-349 352 359
364 371 384 400
438 451 484 493
500 507 509 511
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TABLE 1
Tissue Ori Librar /RNA HYSEQ Librar SEQ ID NOS:
in Source Name
516 522 525 530
532 537 562-563
567-568 580 595
597 603 607 610
612-613 616 620-
622 627 643 653
672-673 675 677-
678
adult spleen Clontech SPLc01 7 9 13 l7 26
37 43
64 75 106 112-114
118 131 163 212
216 218-219 256
259-262 308 314
329-330 349 368
390 392-393 422-
424 427 431 435-
436 451 453 484
500-501 509 525
530 532 535-536
541 592 600 610
613 623 628 631-
632 635 645 654
663 668 672-673
679
bone marrow null STM001 7 43 162 252
256
305 371 427 438
530 607 651 658
stomach Clontech ST0001 67 93 95 135
230
259-262 284-285
289 302-303 308
320 323 390 392-
393 420 428 436
484 507 524-525
530 536 587 631-
632 637
thalamus Clontech THA002 10 18 24 33 47-50
54 58 60 68 90
92-
93 98 100 102
160-
161 180 205 208
229-230 242 259-
262 272 296 302-
305 325 331 342
359 384 386 390
425 511 532 543
572-573 587 602
608-610 612 616
620-621 631-632
660
thymus Clontech THM001 5 12 39-40 43
47-
50 54 56 66 68
70
79 87-88 93 106-
107 131 135 144
162 173-174 177
192 198 205 211
218-219 229 256
281 289-290 293
306 308 314 317-
318 321 323 325
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TABLE 1
Tissue Ori Librar /RNASourceIi1'SEQ LibrarySE ID NOS:
in Name
331-333 347 349-
352 368 371 384
389 420 425 438
440-441 484 487
493 498-499 502
509 530 532 541
554-555 558 597-
599 610 613 616
620-621 624 643
671-673 682
thymus Clontech THMc02 5 8 10 12 25
32 34
37 39 43 45-46
48-
50 53 55-56 61
63
65-67 70 83 85
87-
88 94 106-107
112-
114 116-118 120
131 135 140-142
144 150-152 158-
159.163-165 179
189 208 229 232-
234 256 259-262
273 289-290 302
305 316-318 324-
325 335 349 361
363-364 371 384
389 392-393 421-
424 437-441 443
445-446 451 459-
461 473-474 498
500 504-507 509
518 522 526 530
541 554 564 583
592 600 607 610
a
613 624-625 627
630-632 634 637
643-645 651 667
669 671-673 682
thyroid gland Clontech THR001 6 14-15 19 26
29
32 34 39-40 47-52
56 61-63 66-68
72
75 87 93 95 100
104-106 115 128-
. 131 137 141-142
154 157 162 165
168-169 175 177
182 189 191-193
202-203 211 217-
219 221 229 231-
234 249 254 256
282 289-290 298
302 306-308 314-
316 323-324 327
329-330 342 350
353-358 368 371
377 380 383-384
400 423-424 426
431 436-438 440-
441 446 451 459-
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TABLE 1
Tissue Ori in Librar /RNA HYSEQ Librar SEQ ID NOS:
Source Name
461 475 478 484
487-489 491-492
499-500 502-506
509 518-519 521-
522 530 532-533
541 543 567-568
586 588 597-600
605 607 610 617-
618 620-621 624-
626 63l-632 635
643 651 654 662
668 671-672 680
trachea Clontech TRC001 7 22 38 40 56
68
83 94 229 259-262
289 296 298 360
371-375 438 484
499 511 521 541
571-573 588 613
624 627
uterus Clontech UTR001 l7 36 70 76 103
106 109 112-114
131 150 157 179-
180 189 290 296
308 314 320 329-
330 356 364 366
368 390 395-398
415 438 447 507
509 519 525 529
532 564 620-621
631-632 662 668-
669 682
*The 16 tissue/mRNAs and their vendor sources are as follows: 1) Normal
adult brain mRNA (Invitrogen), 2) Normal adult kidney mRNA (Invitrogen),
3) Normal fetal brain mRNA (Invitrogen), 4) Normal adult liver mRNA
(Invitrogen), 5) Normal fetal kidney mRNA (Invitrogen), 6) Normal fetal
liver mRNA (Invitrogen), 7) normal fetal skin mRNA (Invitrogen), 8) human
adrenal gland mRNA (Clontech), 9) Human bone marrow mRNA (Clontech), 10)
Human leukemia lymphoblastic mRNA (Clontech), 11) Human thymus mRNA
(Clontech), 12) human lymph node mRNA (Clontech), 13) human so\spinal cord
mRNA (Clontech), 14) human thyroid mRNA (Clontech), 15) human esophagus
mRNA (BioChain), 16) human conceptional umbilical cord mRNA (BioChain).
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
685 gi183150 Homo Sapienschorionic somatomammotropin320 100
CS-5
685 gi181127 Homo Sapienschorionic somatomammotropin275 96
precursor
685 gi183153 Homo Sapienschorionic somatomammotropin275 96
CS-2
686 gi183178 Homo SapienshGH-V2 1033 78
686 gi183153 Homo Sapienschorionic somatomammotropin710 87
CS-2
686 gi387024 Homo Sapiensplacental facto en hormone710 87
precursor
688 gi183178 Homo SapienshGH-V2 1051 79
688 gi181121 Homo Sapienschorionic somatomammotropin788 95
688 gi183151 Homo Sapienschorionic somatomammotropin788 95
CS-1
689 gi12653501Homo SapiensSimilar to serine (or 1242 99
cysteine) proteinase
inhibitor, Glade F (alpha-2
antiplasmin,
pigment epithelium derived
factor).
member 1
689 gi15217079Homo Sapienspigment epithelium-derived1242 99
factor
689 gi189778 Homo Sapienspigment epithelial-differentiating1242 99
factor
690 gi17128288synthetic Primer 1 1150 99
construct
690 gi20269957Sus scrofaphospholipase C delta 1033 88
4
690 gi21307610Mus musculusphospholipase C delta 909 77
4
691 gi17864023Homo SapiensKCCR13L 3524 100
691 gi21483462DrosophilaLD44686p 533 36
melano
aster
691 gi21741717Ory~a sativao'991113_30.22 127 29
692 gi17428818Ralstonia GALA PROTEIN 3 117 32
solanacearum
692 gi21536497.~rabidopsisF-box protein family, 115 30
thaliana AtFBL4~
692 gi12581504TrypanosomeGUl 115 33
brucei
693 gi437662 Oryctolagusinterleukin-8 receptor 194 61
cuniculus subtype B
693 gi186378 Homo sapiensinterleukin 8 receptor 178 57
B
693 gi1109691Homo Sapiensinterleulsin-8 receptor178 57
type B
694 13335098 Homo sapiensCD39L2 2520 100
694 gi11230487Rattus NTPDase6 2065 86
norvegicus
694 gi5139519Mus musculusnucleoside diphosphatase1008 53
(ER-UDPase)
695 gi21928620Homo sapiensseven transmembrane 1858 100
helix receptor
695 gi16566319Homo SapiensG protein-coupledreceptor1843 99
695 gi6644328Rattus orphan G protein-coupled822 50
norvegicusreceptor
GPR26
696 gi7110216Homo sapiensC-type lectin-like receptor-1851 99
696 gi7109731Homo SapiensC-type lectin-like receptor-2256 31
696 gi20381202Mus musculusSimilar to C-type (calcium196 27
dependent,
carbohydrate recognition
domain) lectin,
superfamily member 12
697 gi22449809Chaoborus cytochrome oxidase I 50 44
trivitattus
697 gi2351328Newcastle fusion protein 59 44
disease
virus
697 gi21311450Galleria antifungal peptide gallerimycin55 33
i
mellonella
698 gi18089247Homo SapiensSimilar to ectonucleoside2104 100
triphosphate
diphosphohydrolase 5
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
698 gi3335102Homo SapiensCD39L4 2104 100
698 gi15076827Homo SapiensPcph proto-oncogene 2090 99
protein
699 gi151242 Pseudomonasheat shock protein 79 38
aeruginosa
699 gi9950616PseudomonasGroES protein 79 38
aeruginosa
699 gi2564287PseudomonasHsplO protein 79 44
stutzeri
701 gi20521055Homo SapiensStart codon is not identified724 32
701 gi17225457Homo Sapiensautism-related protein 676 32
1
701 gi15145797Sus scrofabasic proline-rich protein156 27
702 gi20810589Homo Sapienssimilar to arsenite 833 99
inducible RNA
associated protein
702 gi9651711Mus musculusarsenite inducible RNA 687 80
associated protein
702 gi17390981Homo SapiensSimilar to RIICEN cDNA 535 59
1110060018
gene
703 gi6624130Rattus similar to 45 kDa secretory2150 100
norvegicusprotein ;
703 gi13241652Rattus supernatant protein 2040 93
norvegicusfactor
703 gi19548982Bos taurustocopherol-associated 1930 90
protein
704 gi13177766Homo SapiensSimilar to presenilins 1761 99
associated
rhomboid-like protein
704 gi15559382Homo Sapienspresenilins associated 1094 98
rhomboid-like _
protein
704 gi7959883Homo SapiensPR~2207 671 82
705 gi1864091Rattus PSD-95/SAP90-associated5005 95
norvegicusprotein-3
705 gi2454510Homo SapiensPSD-95/SAP90-associated1338 55
protein-2
705 gi6979173Homo Sapiensdiscs, large (Drosophila)1011 45
homolog-
associated protein 2
706 gil 1877274Homo SapiensdJ726C3.2 (novel protein)2260 99
706 gi21667210Hozno Sapiensbactericidal/permeability-increasing2260 99
protein-like 1
706 gi20387087~ncorhynchuSLBP (LPs binding protein)/BPI349 26
mylciss (bactericidal/permeability-increasing
protein) like-2
707 gi7291716DrosophilaCG11388-FA 648 39
melanogaster
707 gi16768190DrosophilaGH22974p 647 39
melanogaster
707 gi3954938Homo Sapiensacetylglucosaminyltransferase-like171 23
protein
708 gi14334082Mus musculusthymus LIM protein TLP-A479 87
708 gi14334084Mus musculusthymus LIM protein TLP-B397 79
708 gi487284 Rattus CRP2 (cysteine-rich 367 75
norvegicusprotein 2)
710 gi556299 Mus musculusalpha-2 type IV collagen8129 83
710 gi30076 Homo Sapiensalpha-2 chain precursor5916 100
(AA -25 to 1018)
(3416 is 2nd base in
codon)
710 115991848Homo SapiensA type IV collagen 4239 51
711 gi7861733Homo Sapienslow density lipoprotein2583 99
receptor related 1
protein-deleted in tumor
711 gi8926243Mus musculuslow density lipoprotein2409 91
receptor related 6
protein LRP1B/LRP-DIT
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
711 gi438007 Gallus alpha-2-macroglobulin 1419 63
gallus receptor 7
712 gi17298315Homo Sapienscandidate tumor suppresser848 100
protein
712 gi7861733Homo sapienslow density lipoprotein848 100
receptor related
protein-deleted in tumor
712 gi8926243Mus musculuslow density lipoprotein731 83
receptor related
protein LRP1B/LRP-DIT
713 gi16877754Homo sapiensSimilar to RIKEN cDNA 574 56
4930434H03
gene
713 gi20071811Mus musculusSimilar to RIKEN cDNA 493 60
4930434H03
gene
713 gi1340174Homo sapienstype III procollagen 97 40
(aa 892-1023)
714 gi157409 Drosophilafat protein 1802 31
melanogaster
714 gi4887715Drosophilaadherin 1500 36
melanogaster
714 gi1107687Homo Sapienshomologue of Drosophila1514 30
Fat protein
_ gi157409 Drosophilafat protein 1808 31
715 melanogaster
715 gi4887715Drosophilaadherin 1500 36
melanogaster
715 i 1107687Homo Sapienshomolo a of Drosophila 1514 30
Fat protein
716 117865311Homo Sapiensdipeptidyl peptidase-like2562 99
protein 9
716 gi3513303Homo Sapiens826984_1 2700 98
716 gi11095188Homo Sapiensdipeptidyl peptidase 1397 53
8
717 gi2689444Homo Sapiens~NF134~ 1160 54
717 gi21314~977Homo SapiensSimilar to zinc finger 1038 51
protein 17 (HPF3,
K~X 10)
717 gi 13543419Homo SapiensSimilar to zinc finger 1000 51
protein 304
718 gi7582294Homo SapiensBM-011 881 100
718 gi13937769Homo SapiensSimilar to RIICEN cDNA 781 98
1200013F24
ene
718 ' 178997 Homo Sapiensarginine-rich nuclear 224 38
protein
719 gi1620870Ciona myoplasmin-C1 412 28
intestinalis
719 gi7416980Argopectenmyosin heavy chain catch279 23
irradians (smooth)
muscle specific isoform
719 gi7416982Argopectenmyosin heavy chain cardiac279 23
irradians muscle
specific isoform 1
720 gi13872813Homo Sapiensfibulin-6 1376 100
4
720 gi14575679Homo Sapienshemicentin 1372 99
0
720 gi3328186Caenorhabditishemicentin precursor 1695 30
elegans
721 gi3822553Gallus nuclear calmodulin-binding1492 64
gallus protein
721 gi3329496Mus musculusheterogenous nuclear 1501 45
ribonucleoprotein U
721 gi624918 Rattus SP120 1498 45
norvegicus
722 gi17223626Homo SapiensATP-binding cassette 7966 99
A10
722 '17223624Homo SapiensATP-binding cassette 5160 61
A9
722 gi17223622Homo SapiensATP-bindin cassette 5108 61
A6
723 gi13374079Homo SapiensTAFII140 protein 3677 99
723 gi13374178Mus musculusTAFII140 protein 3202 84
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
723 gi205686 Rattus heavy neurofilament 335 26
norvegicussubunit
724 gi17429038Ralstonia PROBABLE ACYL-COA 661 61
solanacearumDEHYDROGENASE
OXIDOREDUCTASE PROTEIN
724 gi9948609Pseudomonasprobable acyl-CoA dehydrogenase619 62
aeruginosa
724 gi13421911Caulobacteracyl-CoA dehydrogenase 559 59
crescentusfamily protein
CB 15
725 gi6752658Homo Sapiensepidermal growth factor3055 99
repeat containing
protein
725 gi16040981Mus musculusPOEM 884 51
725 ' 15430246Mus musculusnephronectin short isoform884 51
726 gi6531661CaenorhabditisL1N-41A 844 50
elegans
726 gi6531663CaenorhabditisLIN-41B 844 50
elegans
726 gi 12407367Homo Sapienstripartite motif protein769 30
TRIM2
727 gi1504026Homo Sapienssimilar to C.elegans 5833 99
protein (Z37093)
727 gi2896796Homo SapiensD1013901 5115 99
727 gi2522322Homo SapiensPTPLl-associated RhoGAP1497 36
728 gi13274120Homo sapienSdJ55C23.5.1 (vanin 3, 1467 99
isoform 1)
728 gi7160973Homo sapiensVNN3 protein 1213 96
728 gi6102996Mus musculusVanin-3 1018 79
729 gi9581879Homo Sapiensdisintegrin metalloproteinase5723 99
with
thrombospondin repeats
729 gi19171176Homo Sapiensmetalloprotease disintegrin1669 50
15 with
thrombospondin domains
729 gi11095299Rattus ADA1VITS-1 1772 40
norve icus
730 gi21063967DrosophilaAT05453p 396 32
melanogaster
730 gi5911409Drosophilafu~~y 396 32
melanogaster
730 gi2564657DrosophilaFu~~y 396 32
melano
aster
731 gi15217171Homo SapiensCD81 partner 3 2302 100
731 gi15488017Homo sapiensEWI2 2302 100
731 gi15593237Mus musculusimmunoglobulin superfamily2186 92
receptor
PGRL
732 115217171Homo SapiensCD81 partner 3 3200 100
732 gi15488017Homo SapiensEWI2 3200 100
732 gi15593237Mus musculusimmunoglobulin superfamily2867 88
receptor
PGRL
733 gi15217171Homo SapiensCD81 partner 3 1303 96
733 gi15488017Homo SapiensEWI2 1303 96
733 gi22266726Homo SapiensLIR-D1 precursor 1303 96
734 121748480Homo SapiensFLJ00271 protein 605 100
734 gi22266726Homo SapiensLIR-D1 precursor 514 79
734 gi15217171Homo SapiensCD81 partner 3 514 79
735 gi2196872Homo SapiensLsc homologue 203 30
735 11389756 Mus musculusLsc 199 31
735 gi11276027Rattus LSC 199 31
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
norvegicus
736 gi14336728Homo Sapienspossible integral membrane331 32
736 gi18043242Mus musculusRIKEN cDNA 2400010615 331 31
ene
736 gi8895014Hepatitis HBsAg 68 48
B
virus
737 gi20071204Mus musculusSimilar to paraspeckle 185 28
protein 1
737 gi18104577Homo Sapiensparaspeckle protein 175 27
1 alpha isoform
737 gi13528666Homo SapiensSimilar to splicing 179 31
factor
proline/glutamine rich
(polypyrimidine
tract-binding protein-associated)
738 gi12002000Homo SapiensMy029 protein 415 100
738 gi348140 Human T- rex 68 39
lymphotropic
virus 2
738 gi404041 Human T- rex protein 68 39
lymphotropic
virus 2
739 gi4680090Human envelope glycoprotein 89 31
immunodeficien
cy virus
type 1
740 gi21627272DrosophilaCG12765-PA 166 38
melanogaster
740 gi19528077DrosophilaAT24025p 166 38
melanogaster
740 gi1066820Murray nonstructural protein 66 28
Valley
encephalitis
virus
741 gi9916 Plasmodiumliver stage antigen 468 26
falciparum
741 gi1747 Oryctolagustrichohyalin 414 24
cuniculus
741 1295941 Ovis criestrichohyalin 395 24
742 gi98454=85Homo Sapiensprotocadherin-9 6235 100
742 gi15054521Homo Sapiensprotocadherin-S 3390 58
742 gi13161060Homo Sapiensprotocadherin 11 3382 58
743 gi5688958Homo SapiensPMMLP 2405 100
743 121594625Mus musculusRII~EN cDNA 4931406N15 2241 92
gene
743 gi16797814~Drosophilaphosphomannomutase 45A 1194 51
melanogaster
744 gi21734445Rattus BMP/Retinoic acid-inducible3987 94
norvegicusneurai-
specific protein-2
744 gi20988899Mus musculussimilar to deleted in 2952 70
bladder cancer
chromosome region candidate
1
744 gi21734447Rattus BMP/Retinoic acid-inducible2951 70
norvegicusneural-
specific protein-3
745 12739353 Homo SapiensZNF91L 2075 69
745 gi1017722Homo Sapiensrepressor transcriptional2044 71
factor
745 gi4559318Homo SapiensBC273239_1 2031 67
746 11017722 Homo Sapiensrepressor transcriptional2144 73
factor
746 gi2739353Homo SapiensZNF91L 2054 70
746 gi186774 Homo Sapienszinc finger protein 2035 70
747 119683999Homo Sapienscoated vesicle membrane1010 99
protein
747 gi1212965Homo Sapienstransmembrane protein 1010 99
747 gi1213221Rattus transmembrane protein 1006 98
norvegicus
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
748 gi1199524Homo Sapiensacidphosphatase 2b36 98
748 gi34263 Homo Sapiensacid phosphatase precursor2036 98
protein
748 gi13111975Homo Sapiensacid phosphatase 2, 2032 98
lysosomal
749 gi15625570Homo Sapienscentaurin betas 2970 83
749 14688902Homo Sapienscentaurin beta2 1708 64
749 1436228 Homo SapiensStart codon is not identified1387 70
750 gi10197642Homo SapiensMDS022 647 100
750 gi19683046DictyosteliumHYPOTHETICAL 21.8 KDA 94 26
discoideum PROTEIN.
3/101
750 gi6841554Homo SapiensHSPC166 93 24
751 gi5630080Homo Sapienssimilar to HUB 1; similar696 48
to BAA24380
(PID:g2789430)
751 gi2789430Homo Sapiensrepressor protein 702 39
7 gi18614026Homo Sapienszinc finger DNA binding1004 41
51 protein p71
_ gi12140290Homo SapiensbA12M19.2.1 (vacuolar 2885 92
752 protein sorting
protein 16 (VPS16))
752 gi11345382Homo sapiensvacuolar protein sorting2885 92
protein 16
752 gi19343731Mus musculusvacuolar protein sorting2803 89
16 (yeast
homology
753 120987877Mus musculussimilar to Nogo receptor905 58
753 gi9280025Macaca Nogo receptor 808 49
fascicularis
753 gi15080005Homo Sapiensno o receptor 796 4~8
754 gi 177870Homo Sapiensalpha-2-macro lobulin 2714 39
precursor
754 gi579592Homo sapiensalpha 2-macroglobulin 2708 39
690-730
754 gi579594Homo Sapiensalpha 2-macro lobulin 2700 39
690-740
755 gi4929790Homo Sapiensangiopoietin-related 1423 89
protein 3
755 ' 13159474Homo SapiensCG006-alt2 1416 88
755 gi5639997Mus musculusangiopoietin-related 1109 77
protein 3
756 '200057 Mus musculusneuronal glycoprotein 4821 87
756 gi563133Rattus BIG-1 protein 4778 87
norvegicus
756 gi1016012RattuS neural cell adhesion 3867 68
norvegicus protein BIG-2
precursor
757 gi6273399Homo sapiensmelanoma-associated 344 33
antigen MG50
757 gi1504040Homo Sapienssimilar to D.melanogaster344 33
peroxidasin(U11052)
757 gi14495561Homo Sapiensbrain tumor associated 324 27
protein LRRC4
758 gi6273399Homo Sapiensmelanoma-associated 344 33
antigen MG50
758 gi1504040Homo Sapienssimilar to D.melanogaster344 33
peroxidasin(Ul 1052)
758 gi14495561Homo Sapiensbrain tumor associated 329 26
protein LRRC4
759 gi5525078Rattus seven transmembrane 5062 72
norvegicus receptor
759 121929093Homo Sapiensseven transmembrane 1712 88
helix receptor
759 gi4164023Bos taurus latrophilin 2 splice 383 27
variant baaaf
760 gi10440398Homo SapiensFLJ00032 protein 1261 57
760 gi11917507Homo SapiensHPF1 protein 1258 60
760 gi13752754Homo Sapienszinc finger 1111 1253 60
761 gi3628757Homo SapiensFICl 1436 54
761 gi13097633Homo SapiensSimilar to ATPase, Class1221 60
I, type 8B,
member 1
761 gi20147219ArabidopsisAt1g59820/F23H11_14 1637 41
thaliana
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
762 gi11527987Gallus immunoglobulin-like 97 30
gallus receptor CHIR-A
762 gi432214 Human envelope glycoprotein 43 39
gp120
immunodeficien
cy virus
type 1
762 gi15026993Homo SapiensMUCSAC protein 64 38
763 gi11558486Homo SapiensB-cell lymphoma/leukaemia1314 99
11A short
form
763 gi7546791Mus musculusCTIP1 protein 1149 99
763 gi7650184Mus musculusecotropic viral integration1155 95
site 9 isoform
C
764 gi22085890Rattus FHA-HIT 1426 82
norvegicus
764 gi21430028DrosophilaGM01362p 338 40
melanogaster
764 gi21166012Dictyostelium2410016G21RIK PROTEIN 279 26
discoideum
765 gi22085890Rattus FHA-HIT 214 88
norvegicus
765 gi5764101Homo Sapienspolynucleotide kinase-3'-phosphatase95 50
765 gi5712131Homo SapiensDEM1 protein 93 50
766 gi22085890Rattus FHA-HIT 278 89
norvegicus
766 gi5764101Homo sapienspolynucleotide Icinase-3'-phosphatase109 46
766 gi5712131Homo SapiensDEM1 protein 107 46
768 gi 15186770Homo sapienslysyl oxidise-like protein1818 96
768 gi14009597Homo Sapienslysyl oxidise-like 3 1818 96
protein
768 gi15030096Mus musculusSimilar to lysyl oxidise-like1715 92
2
769 gi3954938Homo Sapiensacetylglucosaminyltransferase-like2298 70
protein
769 gi3954978Mus musculusacetylglucosaminyltransferase-like2298 70
protein
769 gi10834722Homo SapiensPP5656 892 91
770 gi7209723Homo SapiensVdD-repeat like Scqucnce2476 99
770 gi8217485Homo sapiensdJ1092A11.3 (WD rcpcit 2473 99
domain)
770 gi7209721Mus musculusDD57 2243 88
771 gi18676632Homo SapiensFLJ00215 protein 1943 99
771 gi18447198DrosophilaGH09355p 140 19
melanogaster
771 gi295671 Saccharomycesselected as a weak suppressor119 22
of a mutant
cerevisiaeof the subunit AC40
of DNA dependant
RNA polymerise I and
III
772 gi10799166Homo Sapiensprotein kinase Njmu-Rl 1915 99
772 gi21104460Homo SapiensOIC/SW-CL.19 549 100
772 gi14290030Human pol protein 68 30
immunodeficien
cy virus
type 1
773 gi4186023Homo SapiensCDS2 protein 2376 100
773 gi19344052Homo Sapienssimilar to PHOSPHATIDATE2376 100
CYTIDYLYLTRANSFERASE
2 (CDP-
DIGLYCERIDE SYNTHETASE
2)
(CDP-DIGLYCERIDE
PYROPHOSPHORYLASE 2)
(CDP-
DIACYLGLYCEROL SYNTHASE
2)
(CDS 2) (CTP:PHOSPHATIDATE
CYTIDYLYLTRANSFERASE
2) (CDP-
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TABLE 2 A
SEQ Hit ID Species Description ~ Percentage
S
ID scoreidenti
DAG SYNTHASE 2) (CDP-DG
SYNTHETASE 2)...
773 gi13277972Mus musculusSimilarto CDP-diacylglycerolsynthase2289 96
(phosphatidate cytidylyltransferase)
2
774 gi17862928DrosophilaSD03549p 125 35
melanogaster
774 gi18077663Mus musculuscockayne syndrome group117 38
A
774 gi14091657Mangifera F6N15.8-like protein 107 29
indica
776 gi18676664Homo SapiensFLJ00231 protein 1473 99
776 gi163b3748Homo Sapienstweety-like protein 1053 41
2
776 116303750Musmusculustweetyhomolo 2 987 39
777 gi8118032Homo Sapiensorphan G-protein coupled939 98
receptor
777 gi16877193Homo SapiensG protein-coupled receptor,939 98
family C,
group 5, member C
777 gi9588669Homo SapiensGPRCSC 939 98
778 gi20380605Mus musculusRIKEN cDNA 8430424D23 836 91
ene
778 gi16769562DrosophilaLD38910p , 333 47
melanogaster
778 gi7302978DrosophilaCG8441-PA 333 47
melanogaster
779 gi16041781Homo SapiensSimilar to RII~EN cDNA 776 99
0710001005
gene
779 gi21430012DrosophilaGH27470p 333 53
melanogaster
779 gi15074454Sinorhi~obiumC~NSERVED HYP~THETICAL 239 43
meliloti PROTEIN
780 gi13959018Homo Sapiensendothelial cell-selective902 100
adhesion
molecule
780 gi13991773Mus musculusendothelial cell-selective643 70
adhesion
molecule
780 11814277 Homo SapiensA33 antigen precursor 229 34
781 gi8164184Homo Sapiens22kDa peroxisomal membrane1013 100
protein-
like
781 ' 15422171Homo sapiens22 kDa peroxisomal membrane1013 100
protein 2
781 gi297437 Rattus peroxisomal membrane 798 76
protein
norvegicus
782 gi7621329StreptococcusSic1.245 214 39
pyogenes
782 gi7620883StreptococcusSic1.23 215 39
pyogenes
782 gi7620875StreptococcusSic1.19 215 39
pyogenes
783 gi62877 Gallus type VI collagen alpha-2751 41
gallus subunit ~
preprotein
783 gi62882 Gallus type VI collagen subunit751 41
gallus alpha2
783 gi211616 Gallus type VI collagen, alpha-2747 45
gallus subunit
784 gi17945608DrosophilaRE26969p 829 48
melano
aster
784 gi3877350Caenorhabditiscontains similarity 572 38
to Pfam domain:
elegans PF01598 (Sterol desaturase),
Score=307.6, E-value=4.7e-89,
N=1
784 gi3877351Caenorhabditiscontains similarity 546 38
to Pfam domain:
elegans PF01598 (Sterol desaturase),
Score=303.0, E-value=l.le-87,
N=1
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
785 gi17066106Homo SapiensNovex-3 Titin Isoform 8832 99
785 gi21238628Sparisoma thin-like protein 519 62
viride
785 gi21238630Sparisoma titin-like protein 519 62
aurofrenatum
787 gi2230840Ginkgo ndhB 54 54
biloba
787 gi2230828Dioon edulendhB 52 50
787 gi9279991Sequoia maturase 60 36
sempervirens
788 gi18676610Homo SapiensFLJ00204 protein 204 27
788 gi3002588Mus musculusPlenty of SH3s; POSH 206 25
788 gi14b7665Mus musculusSH3P3 134 45
789 gi18676610Homo SapiensFLJ00204 protein 262 27
789 13002588 Mus musculusPlenty of SH3s; POSH 220 25
789 gi1407665Mus musculusSH3P3 140 33
790 gi182483 Homo Sapiensprefibroblast collagenase531 88
inhibitor
790 gi490094 Homo SapiensTIMP 531 88
790 gi189382 Homo Sapienscollagenase inhibitor 531 88
791 gi7110216Homo SapiensC-type lectin-like receptor-1851 99
791 gi7109731Homo SapiensC-type lectin-like receptor-2256 31
791 gi1902982Bos tauruslectin-like oxidized 303 31
I,DL receptor
792 gi5802604Cavia porcellusUDP glucuronosyltransferase1783 73
UGT2A3
792 gi19387963Mus musculusRIKEN cDNA 2010321J07 1709 69
gene
792 '4753766 Homo SapiensUDP glucuronosyltransferase1598 67
793 gi3688090Homo SapiensR32611_2 786 91
793 16841228 Homo sapiensHSPC289 638 78
793 gi21618688Mus musculusRIKEN cDNA 5830498014 445 52
gene
794 gi9963861Homo sapiensCytl9 1729 99
794 gi15488645Mus musculusmethyltransferase Cytl91555 76
794 gi18150409Rattus S-adenosylmethionine:arsenic1516 76
norvegicus(III)
methyltransferase
795 '11877243Homo SapiensSSFl/P2~'11 chimeric 1957 95
protein
795 gi21619996Homo Sapienspeter pan homolo (Drosophila)2080 99
795 gi14602631Homo Sapienspeter pan (Drosophila) 2080 99
homolog
796 gi20330550Homo SapiensNK inhibitory receptor 799 98
precursor
796 gi20380183Homo SapiensSimilar to CMRF35 leukocyte727 92
immunoglobulin-like
receptor
796 gi20381405Homo Sapienssimilar to CMRF35 leukocyte423 57
immunoglobulin-like
receptor; CMRF35
antigen
797 120330550Homo SapiensNK inhibitory receptor 799 98
precursor
797 gi20380183Homo Sapienssimilar to CMRF35 leukocyte727 92
immunoglobulin-like
receptor
797 gi20381405Homo Sapienssimilar to CMRF35 leukocyte423 57
immunoglobulin-like
receptor; CMRF35
antigen
798 gi20330550Homo SapiensNK inhibitory receptor 1469 94
precursor
798 gi20380183Homo Sapienssimilar to CMRF35 leukocyte690 84
immuno lobulin-like
receptor
798 gi20330544Mus musculuspolymeric immunoglobulin416 52
receptor 3
precursor
799 gi18307481Homo Sapiensphosphoinositide-binding2122 100
proteins
799 gi3930781Homo Sapiensconnector enhancer of 346 34
KSR-like protein
CNKl
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
799 gi4151807Rattus membrane-associated 455 37
norvegicusguanylate kinase-
interacting protein
2 Maguin-2
800 gi15929988Homo SapiensSimilar to TLH29 protein417 89
precursor
800 gi11493982Homo SapiensTLH29 protein precursor274 72
800 120147034Mus musculusinterferon stimulated 235 68
ene 12
801 gi15929988Homo SapiensSimilar to T'LH29 protein445 100
precursor,
clone MGC:21991 IMAGE:4398045,
mRNA, complete cds.
801 AAW54040 Homo SapiensHuman interferon-inducible432 97
protein,
HIFI.
801 gi11493982Homo SapiensTLH29 protein precursor303 70
(TLH29)
mRNA, complete cds.
802 gi12082725Mus musculusB cell phosphoinositide3561 84
3-kinase adaptor
802 gi12082723Gallus B cell phosphoinositide2840 69
gallus 3-kinase adaptor
802 gi20987486Homo Sapienssimilar to B cell phosphoinositide1830 97
3-
kinase adaptor
803 gi7959809Homo SapiensPR01082 545 100
803 gi7767407Avian 5a protein 61 26
infectious
bronchitis
virus
803 gi15073792SinorhizobiumPUTATIVE FOSMIDOMI'C1N 71 38
meliloti RESISTANCE ANTIBIOTIC
RESISTANCE TRANSMEMBRANE
PROTEIN
804 115384=843Homo SapiensNTB-A receptor 1700 100
804 gi1538484~1Homo Sapiensactivatin Nl~receptor 1687 99
804 gi9887089Mus musculuslymphocyte antigen 108 637 44
isoform 1
805 gi17979255ArabidopsisAT5g495501I~6M13_10 211 72
thaliana
805 gi10177621Arabidopsisphytoene dehydrogenase-like195 75
thaliana
805 gi14023915Mesorhizobiumphytoene dehydrogenase 182 62
loti
806 gi14270364~Mus musculusEpigon protoin 386 71
806 gi755468 Xenopus transmembrane protein 120 36
laevis
806 gi7799191Mus musculustomoregulin-1 125 52
807 gi14270364Mus musculusEpigen protein 386 71
807 gi755468 Xenopus transmembrane protein 120 36
laevis
807 gi7799191Mus musculustomore lin-1 125 52
808 gi14~270364Mus musculusEpi en protein 386 71
808 gi755468 Xenopus transmembrane protein 120 36
laevis
808 gi7799191Mus musculustomoregulin-1 125 52
809 gi3068592Mus musculuspunt 201 41
809 gi22003417Daniorerioneogenin 193 40
809 gi1881477Mus musculusneo enin protein 167 33
810 ' 15072404Raja erinaceaor anic solute transporter92 41
beta
810 gi143486 Bacillus levansucrase 59 37
subtilis
810 gi143484 Bacillus levansucrase (sacB) 58 35
subtilis
811 gi18650588Homo Sapiensretinoic acid early 1124 99
transcript 1
811 gi13128925Homo SapiensULBP2 protein 1070 94
811 gi21961213Homo sapiensUL16 binding protein 1070 94
2
812 gi9280405Homo sa adlican 1372 46
iens
812 gi3328186Caenorhabditishemicentin precursor 475 29
elegans
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
812 114575679Homo Sapienshemicentin 493 28
814 gi9280405Homo Sapiensadlican 2438 35
814 gi14575679Homo Sapienshemicentin 688 25
814 gi3328186Caenorhabditishemicentin precursor 586 26
elegans
815 gi21619635Homo Sapienssimilar to Alu subfamily270 60
SQ sequence
contamination warning
entry
815 gi6650810Homo SapiensPR01902 264 63
815 gi3002527Homo Sapiensneuronal thread protein247 62
AD7c-NTP
816 gi6707435Homo Sapiensapolipoprotein AS 1864 100
816 gi12240284Mus musculusapolipoprotein AS 1310 72
816 gi6707431Rattus apolipoprotein AS 1293 72
norvegicus
817 gi6707435Homo Sapiensapolipoprotein AS 1864 100
817 gi12240284Mus musculusapolipoprotein A5 1310 72
817 gi6707431Rattus apolipoprotein AS 1293 72
norvegicus
818 gi12751065Homo SapiensPNAS-25 360 81
818 gi1208732Drosophilaovary2 276 33
melanogaster
818 gi21428518DrosophilaLD33046p 275 33
melanogaster
819 gi5771420Homo Sapiensgroup IID secretory 852 100
phospholipase A2
819 16453793 Homo sapiensphospholipase A2 846 99
819 gi10862736Homo SapiensdJ169O23.3 (phospholipase846 99
A2 group
IID)
820 gi6015448Hylobates dopamine receptor D4 79 35
lar
820 gi5059331Human major capsid protein 85 29
papillomavirus
type 83
820 gi 13278034Mus musculusSimilar to selectin, 83 35
platelet (p-selectin)
ligand
821 gi12654~883Homo SapiensrTS beta protein 2112 96
821 gi 1150421Homo SapiensrTSbeta 2112 96
821 gi11094~019Homo SapiensRTS beta 2106 96
822 gi12803167Homo Sapiensnucleosome assembly 1728 99
protein 1-like 1
822 gi189067 Homo SapiensNAP 1728 99
822 gi220496 Mus musculusnucleosome assembly 1718 98
protein-1
823 gi 13432042Homo Sapiensintegrin-linked kinase-associated2009 99
serine/threonine phosphatase
2C
823 gi20072498Mus musculusSimilar to protein phosphatase1926 94
2C
823 gi3777604Rattus protein phosphatase 1922 94
norvegicus2C
824 gi7768636Xenopus ICielin 242 36
laevis
824 gi6979313Mus musculuscysteine-rich repeat-containing183 30
protein
GRIM 1
824 gi11527817Homo SapiensCRIM1 protein 178 30
825 gi21928259Homo Sapiensseven transmembrane 1023 100
helix receptor
825 gi18480746Mus musculusolfactory receptor MOR261-10864 84
825 gi18480744Mus musculusolfactoryreceptor MOR261-9858 82
826 gi21928655Homo sapiensseven transmembrane 1458 93
helix receptor
826 gi18480746Mus musculusolfactory receptor MOR261-101280 79
826 118480744Mus musculusolfactory receptor MOR261-91258 78
827 16760369 Mus musculusODZ3 364 95
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
827 gi4760780Mus musculusTen-m3 364 95
827 gi5307761Danio rerioten-m3 310 78
828 gi21205852Homo SapiensT-cell activation Rho 3756 100
GTPase activating
protein; TA-GAP
828 gi21205854Homo SapiensT-cell activation Rho 2850 100
GTPase activating
protein splice variant
1; TA-GAP
828 gi16265938Homo SapiensFKSG15 24_3998
829 gi10432396Homo sapiensdJ947L8.1.5 (novel CUB 383 62
domain protein)
829 gi14787176Mus musculusCSMD1 373 61
_ gi14787181Homo SapiensCUB and sushi multiple 369 60
829 domains protein
1 short form
830 gi10432396Homo sapiensdJ947L8.1.5 (novel CUB 383 62
domain protein)
830 gi14787176Mus musculusCSMD1 373 61
830 gi14787181Homo SapiensCUB and sushi multiple 369 60 '
domains protein
1 short form
831 gi532124 Dictyosteliummyosin IC 525 41
discoideum
831 gi6472600Chara corallinaunconventional myosin 511 43
heavy chain
831 gi9453839Chara corallinamyosin 511 43
832 gi8953751Arabidopsismyosin heavy chain MYA2646 40
thaliana
832 gi6472600Chara corallinaunconventional myosin 646 39
heavy chain
832 '9453839 Chara corallinamyosin 646 39
833 gi17066528Canis familiarisimmunoglobulin gamma 42 38
heavy chain C
833 gi21113238XanthomonasIS1595transposase 50 43
campestris
pv.
campestris
str.
ATCC 33913
833 gi16413516Listeria similar to B. subtilis 56 37
innocua YIaI protein
834 gi7248845Homo Sapienstestican-1 2429 99
834 gi793845 Homo Sapienstestican 2429 99
834 gi21265163Homo Sapienssparc/osteonectin, cv,~cv2425 99
and kazal-lilts
domains proteo lycan
(testican)
835 gi12804465Homo Sapiensprostate cancer overexpressed1632 59
gene 1
835 gi3462515Homo SapiensPB39 1632 59
835 gi 13111981Homo SapiensSimilar to selectively 283 34
expressed in
embryonic epithelia
protein-1
836 gi12804465Homo Sapiensprostate cancer overexpressed1637 59
gene 1
836 gi3462515Homo SapiensPB39 1637 59
836 gi13111981Homo SapiensSimilar to selectively 283 34
expressed in
embryonic epithelia
protein-1
837 gi7689029Homo Sapiensuncharacterized hypothalamus664 100
protein
HBEX2
837 gi17391348Homo SapiensSimilar to brain expressed,664 100
X-linked 1
837 gi9963771Homo Sapiensovarian granulosa cell 664 100
13.0 lcDa protein
hGR74 homolog
838 gi4585574Rattus Slitl 287 35
norvegicus
838 '17380582Homo SapiensSLIT1 isoform B 279 35
838 gi4049587Homo SapiensSlit-2 protein 297 35
839 gi15488920Homo SapiensSimilar to RIKEN cDNA 632 100
2010107623
gene
839 gi19354289Mus musculusRIKEN cDNA 2010107623 570 92
gene
839 12267416 Hepatitis hepatitis delta antigen76 33
D
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
virus
840 gi21619776Homo SapiensSimilar to RIKEN cDNA 2491 100
2600011E07
gene
840 gi20988071Mus musculusSimilar to RIKEN cDNA 921 80
2600011E07
gene
840 gi14531291Mus musculushigh mobility group 87 34
protein isoform I
841 gi21667649Drosophilamyosin binding subunit 231 29
melano of myosin
aster phosphatase
841 gi21392168DrosophilaRE63915p 231 29
melanogaster
841 gi3929221Homo SapiensTRF1-interacting ankyrin-related183 32
ADP-
ribose polymerase
842 gi12408286Homo Sapiensapolipoprotein L-IV 1742 100
splice variant a
842 gi13374351Homo Sapiensapolipoprotein L4 1728 99
842 gi12408285Homo Sapiensapolipoprotein L-IV 1683 98
splice variant b
843 112408286Homo Sapiensapolipoprotein L-IV 1737 99
splice variant a
843 gi13374351Homo Sapiensapolipoprotein L4 1723 99
843 gi12408285Homo sapiensapolipoprotein L-IV 1678 98
splice variant b
844 gi21744725Homo Sapiensglycosyl-phosphatidyl-inositol-MAM2296 100
844 gi7529598Homo SapiensdJ402N21.3 (novel protein1048 100
with
Immuno lobulin domains)
844 gi7529599Homo SapiensdJ402N21.1 (novel protein)662 100
845 gi21744~725Homo Sapienslycosyl-phosphatidyl-inositol-MAM5051 100
845 gi7529598Homo sapienSdJ402N21.3 (novel protein1548 99
with
Immuno lobulin domains)
845 gi7529597Homo SapiensdJ402N21.2 (novel protein1474 100
with MAM
domain)
846 gi4007758Schi~osacoharoconserved protein; similar633 34
myces pombeto S. cerevisiae
YPR144C
846 gi1066493SaccharomycesWeak similarity near 482 32
cerevisiaeC-terminus to RNA
Polymerase beta subunit
(Swiss Prot.
accession number P11213)
and CCAAT-
binding transcription
factor (PIR
accession number A36368)
84=6gi18086412ArabidopsisAt2g17250/T23A1.11 420 44
thaliana
847 gi14701768Homo SapiensVam6/Vps39-like protein3499 96
847 gi14280050Homo SapiensVps39/Vam6-like protein3499 96
847 118857927Mus musculusVPS39 long isoform 3409 93
848 gi3811347Homo Sapienscytosolic phospholipase1209 44
A2 beta
848 gi4886978Homo sapienscytosolic phospholipase1209 44
A2 beta;
cPLA2beta
848 gi190004 Homo Sapiensphosphatidylcholine 512 35
2-acylhydrolase
849 gi7291437DrosophilaCG4071-PA 516 51
melanogaster
849 gi17946619DrosophilaRH31535p 217 42
melanogaster
849 gi21645615DrosophilaCG4071-PB 217 42
melanogaster
850 gi13161409Mus musculusfamily 4 cytochrome 444 73
P450
850 gi5263306Coptotermesfamily 4 cytochrome 200 41
acinaciformisP450
850 gi13182964Mus musculuscytochrome P450 CYP4F13196 38
851 gi13447749Homo Sapiensfibroblast growth factor2475 98
receptor 5
851 gi10944887Homo SapiensFGFR-like protein 2475 98
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
851 gi13183618Homo SapiensFGF homologous factor 2421 97
receptor
852 gi13447749Homo Sapiensfibroblast growth factor2701 99
receptor 5
852 gi10944887Homo SapiensFGFR-like protein 2701 99
852 gi13183618Homo SapiensFGF homologous factor 2647 98
receptor
853 113183618Homo SapiensFGF homolo ous factor 583 98
receptor
853 gi13447749Homo Sapiensfibroblast owth factor 583 98
receptor 5
853 gi10944887Homo SapiensFGFR-like protein 583 98
854 gi643656 Rattus synaptotagmin VII 2035 95
norvegicus
854 gi12667446Rattus synaptotagmin VIIs 2035 95
norvegicus
854 gi6136786Mus musculussynaptotagmin VII 2026 95
855 gi12053709Homo Sapiensa disintegrin-like and 8842 100
metalloprotease
(reprolysin type) with
thrombospondin
type 1 motif, 12
855 gi5923788Homo Sapienszinc metalloprotease 2489 58
ADAMTS7
855 gi19171178Homo Sapiensmetalloprotease disintegrin1598 39
16 with
thrombospondin type
I motif
856 gi15929988Homo SapiensSimilar to TLH29 protein155 86
precursor
856 gi7649139Homo SapienspIFI27-like protein 83 44
856 gi11493982Homo SapiensTLH29 protein precursor83 44
857 gi13542874IVIus musculusSimilar to CGI-67 protein1299 74
857 gi21707079Homo Sapienssimilar to RII~EN cDNA 1278 75
2210412D01
857 gi4929603Homo SapiensCGI-67 protein 1087 81
858 gi13542874Mus musculuSSimilar to CGI-67 protein1299 74
858 gi21707079Homo sapienSsimilar to RII~EN cDNA 1279 73
2210412D01
858 gi4929603Homo SapiensCGI-67 protein 1087 81
859 gi21595166Mus musculuSRIICEN cDNA 4933425F03 1823 83
gene
859 gi16359267Mus musculusSimilar to RIKEN cDNA 1822 83
4933425F03
gene
859 gi21619888Homo SapiensSimilar to RII~EN cDNA 1542 98
4933425F03
ene
860 121595166MuS musculusRII~EN cDNA 4933425F03 2278 88
gene
860 gi16359267Mus muSCUlusSimilar to RIIfEN cDNA 2277 88
4933425F03
gene
860 gi21619888Homo SapiensSimilar to RII~EN cDNA 1958 99
4933425F03
gene
861 gi11493463Homo SapiensPR~2852 301 75
861 gi14189960Homo SapiensPR~0764 271 65
861 gi21104464Homo Sapiens~I~/SW-CL.41 264 70
863 gi21320872Mus musculusCog8 2747 88
863 gi17862986DrosophilaSD07339p 795 45
melano
aster
863 gi5922593Schizosaccharopi008 230 21
myces pombe
864 gi21618851Mus musculusRII~EEN cDNA 2610510L01882 92
gene
864 gi20977573Danio rerioU1 small nuclear ribonucleoprotein75 32
C
864 gi1562574Mus musculusU1 snRNP-specific protein75 32
C
865 gi17862312DrosophilaLD21841p 646 41
melanogaster
865 gi22294210ThermosynechoWD-40 repeat protein 123 27
coccus
elongatus
BP-1
865 gi886024 ThermomonospPkwA 124 25
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
ora curvata
866 gi3878846CaenorhabditisROSD7.3 119 37
elegans
866 gi1685056Xenopus Pax6 87 24
laevis
866 gi8132389Xenopus paired domain transcription81 23
laevis factor variant
A
867 gi12406973Homo Sapiensalanine-glyoxylate aminotransferase2740 100
2
867 gi1944136Rattus beta-alanine-pyruvate 2255 83
norvegicusaminotransferase
867 gi1000448Rattus Rat kidney AGT2 precursor2208 81
norvegicus
868 112406973Homo Sapiensalanine-glyoxylate aminotransferase1870 98
2
868 gi1944136Rattus beta-alanine-pyruvate 1630 86
norvegicusaminotransferase
868 gi1000448Rattus Rat kidney AGT2 precursor1583 84
norvegicus
869 gi4165315Sus scrofakallilcrein 468 42
869 gi190263 Homo Sapiensplasma prekallikrein 467 38
869 gi8809781Homo Sapiensplasma kallikrein precursor467 38
870 gi17985046Brucella GLYCOSYL TRANSFERASE 137 28
melitensis
870 gi5478237Brucella Bme7 137 28
melitensis
870 gi2090678~MethanosarcinaTransposase 126 25
mazei Goel
871 gi4565840Cnemidophoruscytochrome b oxidase 76 41
ti is
871 gi15023030ClostridiumUncharacterized membrane72 44
acetobutylicumprotein,
ortholog YYAS B.subtilis
871 gi7549241Barbatia cytochrome oxidase subunit71 28
tenera I
872 18705222 Homo SapiensIL-17B receptor 1998 100
872 i924~6433Homo SapiensIL-17 receptor homolog 1996 99
precursor
872 gi9246429Mus musculusIL-17 receptorhomolo 1x04 76
precursor
873 gi18676472Homo sapiensFLJ00133 protein 6475 100
873 gi186764~98Homo sapiensFLJ00146 protein 2352 100
873 gi161467 Strongylocentrofibropellin Ia 1246 38
tus purpuratus
874 gi213198 Petromyzonfibrinogen alpha chain 89 39
marinus
874 gi15292317DrosophilaLD46863p 87 34
melano
aster
874 gi4877921Streptococcusserum opacity factor 81 33
pyogenes precursor
875 gi14249936Homo SapiensSimilar to S-adenosylhomocysteine2582 97
hydrolase-like 1
875 gi17390493Mus musculusS-adenosylhomocysteine 2429 92
hydrolase-like 1
875 gi2852125Homo SapiensS-adenosyl homocysteine2429 92
hydrolase
homolog
876 114279990Homo Sapiensubiquitin UBF-fl 458 100
876 gi6706799Homo SapiensdJ447F3.2.1 (ubiquitin-conjugating214 74
enzyme E2 H10 (isoform
1))
876 gi14043322Homo Sapiensubiquitin carrier protein214 74
E2-C
877 gi20086516Homo Sapiensprominin-related protein4241 99
877 gi20086520Mus musculusprominin-related protein3157 73
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TABLE 2 A
SEQ Hit H) Species Description S Percentage
ID scoreidenti
877 gi19909067Rattus testosterone-regulatedprominin-related2920 69
norvegicusprotein
878 gi 13159480Homo SapiensTranslation may initiate2104 100
at the ATG
codon at nucleotides
40-42 or the ATG at
nucleotides 43-45
878 gi21483846Sus scrofafibrinogen-like protein406 36
2
878 gi9229906Ciona fibrinogen-like protein408 36
intestinalis
879 gi13159480Homo SapiensTranslation may initiate2100 99
at the ATG
codon at nucleotides
40-42 or the ATG at
nucleotides 43-45
879 gi21483846Sus scrofafibrinogen-like protein406 36
2
879 gi9229906Ciona fibrinogen-like protein408 36
intestinalis
880 gi13159480Homo SapiensTranslation may initiate2100 99
at the ATG
codon at nucleotides
40-42 or the ATG at
nucleotides 43-45
880 gi21483846Sus scrofafibrinogen-like protein406 36
2
880 gi9229906Ciona fibrinogen-like protein408 36
intestinalis
881 gi11493483Homo SapiensPR02550 322 66
881 gi7770139Homo SapiensPR01722 318 69
881 gi 1872200Homo Sapiensalternatively spliced 304. 72
product using axon
13A
882 gi10175777Bacillus protease speciEc for 67 34
haloduransphage lambda cII
repressor
882 gi15558903Xenopus Tob 64 51
laevis
882 gi21998835Rattus monocarboxylate transporter67 33
norvegicus8
883 118073362Homo Sapienscystine/ lutamate transporter2552 100
883 gi11493652Homo Sapienscalcium channel bloclcer2552 100
resistance
protein CCBRl
883 gi13924720Homo Sapienscystinelglutamate transporter2552 100
xCT
884 gi507213 Homo Sapiensserine kinase 1797 97
884 gi14252988Homo SapiensSRPI~la protein kinase 1797 97
884 gi3135975Homo SapiensdJ4.22H11.1.1 (Serine 1796 98
I~inase) (isoform 1)
885 gi9837288Homo SapiensC-type lectin 271 54
885 gi6651065Homo Sapienslectin-like NIC cell 271 54
receptor LLT1
885 gi18044358Homo SapiensSimilar to lectin-like 270 57
NIA cell receptor
886 gi22164066Homo sapiensneuroblastoma-amplified7571 99
protein
886 gi5833317Oryzias mixed lineage leukemia-like89 23
latipes protein
886 gi7108717Nicotiana MAR-binding protein 89 31
tabacum MFP1 homolog
887 gi22164066Homo Sapiensneuroblastoma-amplified6897 98
protein
887 gi5833317Oryzias mixed lineage leukemia-like89 23
latipes protein
888 gi17430957Ralstonia HYPOTHETICAL TRANSMEMBRANE453 40
solanacearumPROTEIN
888 gi13421965CaulobacterM20/M25/M40 family peptidase377 38
crescentus
CB15
888 gi2330791Schizosaccharocarboxypeptidases precursor352 33
myces pombe
889 gi11558029Homo Sapiensorganic canon transporter1860 99
889 gi18088251Homo SapiensSimilar to hBOIT for 1206 97
potent brain type
or anic ion transporter
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
889 gi9663117Homo Sapiens_ 1852 99
organic cation transporter
X90 gi344112 synthetic chloramphenicol acetyltransferase57 28
construct and
carboxy terminal fusion
protein
890 gi412284 synthetic carboxy terminal fusion57 28
construct protein
890 gi13122523Barbus ATP synthase 8 56 28
brachycephalus
891 '13375149Homo SapiensdJ1118M15.2 (Novel protein)538 98
891 gi7259265Mus musculuscontains transmembrane 269 48
(TM) region
891 gi1806278Rattus glycoprotein 56 143 35
norvegicus
892 gi16589003Homo Sapiensbromodomain-containing 6353 99
4
892 gi9931486Mus musculuscell proliferation related5635 90
protein CAP
892 gi 18308125Mus musculusbromodomain-containing 5633 90
protein BRD4
long variant
893 gi15420828Homo SapiensNOE3-1 2504 99
893 gi19386926Rattus optimedin form B 2484 98
norvegicus
893 gi19386930Mus musculusoptimedin form B 2484 98
894 gi10336599Xenopus follistatin-related 234 32
laevis protein
894 gi349006 Mus musculusTGF-beta-inducible protein225 29
894 gi20810033Mus musculusfollistatin-like 223 29
895 gi5002565Talcifugu cysteine conjugate beta-lyase1244 55
rubripes
895 gi758591 Homo Sapiensglutamine--phenylpyruvate1201 51
aminotransferase
895 gi154~25868Aedes aegyptikynurenine aminotransferase1188 55
896 gi20522012Homo Sapienssimilar to an actin 1312 57
bundling protein,
dematn.
896 gi2337952Homo sapiensactin-bindin double-zinc-finger1312 57
protein
896 gi21666433Mus musculusactin-binding LIM protein1305 57
1 medium
isoform
898 gi6716518Mus musculusdoublccortin-like kinasc821 52
898 gi21619202Homo sapiensSimilar to doublecortin810 51
and CaM kinase-
like 1
898 gi20152113DrosophilaRE56868p 778 45
melanogaster
899 gi9280108Macaca membrane-associated 1907 97
fascicularisprostaglandin E
synthase-2
899 gi9757960Arabidopsiscontains similarity 396 50
thaliana to glutathione-S-
transferaselglutaredoxin~gene_id:MJC20.
26
899 gi17944528DrosophilaRH17614p 566 42
melanogaster
900 gi4894854Homo Sapienscomplement Clq A chain 1308 99
precursor
900 gi20988805Homo Sapienscomplement component 1308 99
1, q
subcomponent, alpha
polypeptide
900 gi12805247Mus musculuscomplement component 945 70
1, q
subcomponent, alpha
polypeptide
901 gi 10176989Arabidopsiscontains similarity 86 34
thaliana to hedgehog-
interacting protein~gene
id:MYH19.17
901 gi456384 Blastocrithidiaapocytochrome B 41 50
culicis
902 gi2565046Homo sa CAGF28 3775 97
iens
902 '21707458Homo sapiensPAX transcription activation2709 87
domain
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
interacting protein
1 like
902 gi4336734Mus musculusPax transcription activation2473 80
domain
interacting protein
PTIP
903 gi4336734Mus musculusPax transcription activation531 93
domain
interacting protein
PTIP
903 gi14164561Xenopus Swift 467 79
laevis
903 gi12382298Human OrfKlO 48 34
herpesvirus
8
904 gi19353375Mus musculusRII~EN cDNA 1110031I02 745 78
gene
904 gi15929776Homo Sapiensgrowth suppressor 1 137 41
904 gi5805194Rattus leprecan 137 41
norvegicus
905 gi2443352Mus musculusplatelet glycoprotein 150 45
Ib beta
905 gi21355064Homo sapiensplatelet glycoprotein 146 43
Ib beta chain
905 gi306792 Homo sapiensplatelet glycoprotein 146 43
Ib beta chain
precursor
906 gi13991166Homo Sapienssialic acid-binding 1174 100
immunoglobulin-like
lectin-like short splice
variant
906 gi13991167Homo Sapienssialic acid-binding 1174 100
immunoglobulin-like
lectin-like long splice
variant
906 gi14625822Homo SapiensSiglec-Ll 1174 100
907 gi21708018Mus musculusRIKEN cDNA 2700029E10 626 66
gene
907 gi7547035Homo SapiensSGC32445 protein 474 63
907 gi21626575DrosophilaCG30193-PA 457 55
melanogaster
908 '6273399 Homo Sapiensmelanoma-associated 2748 60
anti en MG50
908 gi1504040Homo Sapienssimilar to D.melanogaster2748 60
peroxidasin(U11052)
908 gi531385 Drosophilaperoxidasin precursor 1721 42
melanogaster
909 gi6273399Homo Sapiensmelanoma-associated 2748 60
antigen MG50
909 gi1504040Homo Sapienssimilar to D.melanogaster2748 60
peroxidasin(U 11052)
909 gi531385 Drosophilaperoxidasin precursor 1721 42
melanogaster
910 gi6273399Homo Sapiensmelanoma-associated 2799 59
antigen MG50
910 gi1504040Homo Sapienssimilar to D.melanogaster2799 59
peroxidasin(U11052)
910 gi531385 Drosophilaperoxidasin precursor 1708 41
melanogaster
911 gi18182323Mus musculuscrumbs-like protein 777 31
1 precursor
911 gi6014482Homo SapiensCRB1 754 30
911 gi18175289Homo SapiensCRB1 isoform I precursor754 30
912 gi6650802Homo SapiensPR01848 205 56
912 121104464Homo SapiensOIC/SW-CL.41 188 61
912 gi11493463Homo SapiensPRO2852 175 54
913 gi6808611Homo Sapiens88-kDa Golgi protein 3237 99
913 gi6969980Homo Sapiensgolgin 67 2345 98
913 gi7211438Homo Sapiensgolgin-67 2330 98
914 gi3073'77Homo SapiensCAMP-dependent protein 1957 99
kinase RI-beta
regulatory subunit
914 gi200365 Mus musculuscAMP-dependent protein 1886 94
kinase
regulatory subunit
914 gi15030299Mus musculusSimilar to protein kinase,1881 94
cAMP
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
dependent regulatory,
type I beta
915 gi20306468Mus musculusSimilar to RIKEN cDNA 382 41
2610025P08
gene
915 gi7161798Homo SapiensdJ470B24.1.1 (myeloid/lymphoid130 32
or
mixed-lineage leukemia
(trithorax
(Drosophila) homology;
translocated to, 4
(AF-6) (isoform 1))
915 gi7161797Homo SapiensdJ470B24.1.2 (myeloid/lymphoid130 32
or
mixed-lineage leukemia
(trithorax
(Drosophila) homology;
translocated to, 4
(AF-6) (isoform 2))
916 gi1845577Mus musculusarachidonate 12(S)-lipoxygenase2633 77
916 gi3645913Mus musculus12(S)-li ox enase 2633 77
916 ' 15489302Mus musculusSimilar to arachidonate2631 77
15-lipoxygenase
917 gi15489302Mus musculusSimilar to arachidonate751 78
15-lipoxygenase
917 gi1845577Mus musculusarachidonate 12(S)-lipoxy748 78
enase
917 gi1101886Mus musculusarachidonate lipoxygenase748 78
918 gi15489302Mus musculusSimilar to arachidonate1266 75
15-lipoxygenase
918 ' 1845577Mus musculusarachidonate 12(S)-lipoxygenase1263 75
918 11101886 Mus musculusarachidonate lipoxygenase1263 75
919 gi13661964LeishmaniaL344.3 108 21
maj or
919 gi17135639Nostoc WD-repeat protein 95 21
sp. PCC
7120
919 gi11139242Homo sapiensmeiotic recombination 93 25
protein REC14
920 gi17862298DrosophilaLD21662p 627 42
melanogaster
920 gi2425111Dictyostelium~ipA 122 28
discoideum
920 gi641958 Homo Sapiensnon-muscle myosin B 118 24
921 18132683 Homo Sapienscytokine-like protein 241 64
C17
921 112751073Homo SapiensPNAS-31 74 92
921 gi11323101Saint CroixVP4 79 32
river virus
922 gi8132683Homo sapienscytolcine-like protein 241 64
C17
922 ' 12751073Homo SapiensPNAS-31 74 92
922 gi 11323101Saint CroixVP4 79 32
river virus
923 gi8132683Homo Sapienscytokine-like protein 384 73
C17
923 ' 12751073Homo SapiensPNAS-31 74 92
923 gi216168 Bacteriophagepromoter 3 protein 56 37
SPP1
924 gi8132683Homo sapienscytolcine-like protein 263 98
C17
924 gi1143067Canis familiarisalpha-L-fucosidase 69 59
924 1309444 Mus musculusMRI~ 58 65
925 '8132683 Homo Sapienscytolcine-lilee protein591 100
C17
925 13406819 Mus musculusgrowth factor receptor 64 60
925 gi12724591LactococcusUNKNOWN PROTEIN 41 37
lactis
subsp.
lactis
926 gi17975777Homo Sapiensvesicular inhibitory 2741 99
amino acid
transporter
926 gi13396317Homo SapiensbA122O1.1 (A novel protein2741 99
(ortholog of
the mouse vesicular
inhibitory amino acid
transporter, VIAAT))
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TABLE 2 A
SEQ Hit ID Species Description ~S Percentage
ID scoreidenti
926 gi2587061Rattus vesicular GABA transporter2694 98
norvegicus
927 gi3097285Rattus ZOG 670 39
norvegicus
927 gi802014 Rattus preadipocyte factor 665 39
1
norvegicus
927 113365691Mus musculusdlk (Delta like) 649 39
928 gi6624073Homo Sapienssimilar to hepatitis 1757 93
delta antigen
interacting protein
A ; similar to
AAB05928.1 (PID:g1488314)
928 gi1488314Homo Sapienshepatitis delta antigen274 45
interacting protein
A
928 gi16768374DrosophilaGM03282p 359 37
melanogaster
929 gi4337106Homo SapiensBAT4 864 98
929 gi14250638Homo SapiensSimilar to DNA segment,864 98
Chr 17, human
D6S54E
929 '3941733 Mus musculusBAT4 581 71
930 gi9759107Arabidopsisphosphate/phosphoenolpyruvate289 30
thaliana translocator protein-like
930 gi21536504Arabidopsisphosphate/phosphoenolpyruvate245 27
thaliana translocator-like protein
930 gi8778643ArabidopsisF5011.25 235 29
thaliana
931 '5852981 Homo sapienscardiotrophin-like cytokine1204 99
CLC
931 gi6007641Homo sapiensneurotrophin-1/B-cell 1204 99
stimulating factor-3
931 gi15277895Homo SapiensSimilar to cardiotrophin-like1204 99
cytokine;
neurotrophin-1/B-cell
stimulating factor-3
932 gi22003732Homo sapiensMTLC 853 99
932 gi18490933Homo SapiensSimilar to RIKEN cDNA 846 98
1110020804
gene '
932 gi20453974Mus musculusMT-MC1 718 82
933 gi9958075ArabidopsisPutativo methionine 739 53
aminopeptidase
thaliana
933 gi11320956Arabidopsismethionine aminopeptidase-like739 53
protein
thaliana
933 gi21553973Arabidopsismethionyl aminopeptidase-like717 52
protein
thaliana
934 gi4104963Rattus neurexophilin 4 1493 90
norvegicus
934 11336013 Mus musculusneurexophilin 2 327 65
934 14105164 Homo Sapiensneurexophilin 2 323 65
935 gi15025812ClostridiumMethyl-accepting chemotaxis65 38
protein
acetobutylicumwith HAMP domain
935 gi17224936Trypanosomecorset-associated protein63 31
15
brucei
935 gi15025892ClostridiumRibosome-associated 48 38
protein Y (PSrp-1)
acetobutylicum
936 gi16197625Arabidopsisanaphase promoting complex64 32
subunit 11
thaliana
936 gi10834682Homo SapiensPP3958 74 46
937 gi19387136Homo SapiensPYRIN-containing APAFl-like874 99
protein S
937 gi202806 Rattus vasopressin receptor 561 68
norvegicus
937 gi21410402Mus musculusexpressed sequence AI504961532 67
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
938 gi11321325Homo SapiensLin-7b 1030 100
938 gi20381193Homo SapiensLin-7b protein; likely 1030 100
ortholog of mouse
LIN-7B; mammalian LIN-7
protein 2
938 gi3885828Rattus lin-7-A 1019 98
norvegicus
939 gi14349125Homo Sapiensalpha2-glucosyltransferase738 96
939 gi3513451Rattus potassium channel regulator718 93
norve icus1
939 gi21711799DrosophilaRH44301p 142 32
melanogaster
940 gi12803183Homo Sapienspolypyrimidine tract 1527 91
binding protein
(heterogeneous nuclear
ribonucleoprotein
I)
940 gi32354 Homo Sapiensnuclear ribonucleoprotein1527 91
940 135772 Homo Sapienspolypirimidine tract 1527 91
binding protein
941 gi6752658Homo Sapiensepidermal growth factor3046 99
repeat containing
protein
941 gi16040981Mus musculusP~EM 884 51
941 115430246Mus musculusnephronectin short isoform884 51
942 gi6752658Homo Sapiensepidermal growth factor3036 98
repeat containing
protein
942 gi16040981Mus musculusPOEM 884 51
942 gi15430246Mus musculusnephronectin short isoform884 51
943 i 17980969Homo Sapienssel4-3r protein 5146 99
943 gi11385648Homo SapiensCTCL tumor anti en sel4-33867 99
943 17960216 Homo sapiensRACK-like protein PRI~CBP13124 99
944 gi17980969Homo Sapienssel4-3r protein 3140 99
944 gi13677201Homo sapiensdJ569M23.1.2 (protein 2771 100
kinase C binding
protein l,isoform 2)
944 gi13677198Homo SapiensdJ569M23.1.3 (protein 2638 96
kinase C binding
protein l, isoform 3
(DKFZp564P1772))
945 gi17980969Homo Sapienssel4-3rprotein 3550 84
94.5gi13677201Homo sapiensdJ569M23.1.2 (protein 2771 100
kinase C binding
protein 1, isoform 2)
945 gi13677198Homo SapiensdJ569M23.1.3 (protein 2638 96
kinase C binding
protein 1, isoform 3
(DI~FF~p564P1772))
946 gi17980969Homo Sapienssel4-3r protein 3550 84
946 gi13677198Homo sapiensdJ569M23.1.3 (protein 2380 90
kinase C binding
protein 1, isoform 3
(DICFZp564P1772))
946 gi13677201Homo SapiensdJ569M23.1.2 (protein 2377 90
kinase C binding
protein 1, isoform 2)
947 gi14043211Homo sapiensSimilar to RII~EN cDNA 2410 98
4931428F04
gene
947 gi22204070Macaca metabotropic lutamate 91 42
mulatta receptor 1
947 gi170454 Lycopersiconcell wall hydroxyproline-rich70 39
esculentumglycoprotein
948 gi14972753Streptococcusalcoholdehydrogenase,zinc-containing51 33
pneumoniae
TIGR4
948 gi20152351Avian spike glycoprotein S 68 34
infectious1 subunit
bronchitis
virus
948 gi9658106Vibrio polyhydroxyalkanoic 67 26
cholerae acid synthase
949 gi19387136Homo SapiensPYRIN-containin APAFl-like1738 99
protein 5
949 gi202806 Rattus vasopressin receptor 1037 64
~
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
norvegicus
949 gi21410402Mus musculusexpressedsequence AI504961988 63
950 gi3978472Rattus potassium channel subunit5393 88
norve icus
950 gi20338417Gallus potassium channel subunit4792 88
gallus
950 gi7303760DrosophilaCG12904-PA 981 62
melanogaster
951 gi18147612Homo sa metalloprotease disintegrin3535 99
iens
951 gi21908028Homo Sapiensa disintegrin and metalloprotease3535 99
domain
33
951 gi13157560Homo SapiensdJ964F7.1 (novel disintegrin3078 99
and
reprolysin metalloproteinase
family
protein)
952 gi18606367Mus musculusRIKEN cDNA 4930570003 715 92
gene
952 gi9971130Schizosaccharohuman downs syndrome 72 31
myces pombecritical region-
like
952 gi5708224RhodoblastusLH2alpha5 60 31
acidophilus
953 gi15420879Mus musculusankyrin repeat-containing2053 82
SOCS box
protein 10
953 gi18092200Homo SapiensASB-10 1909 98
953 gi18031949Mus musculusSOCS box protein ASB-18816 45
954 gi491284 synthetic IFN-pseudo-omega 2 799 98
construct
954 gi386800 Homo Sapiensinterferon-alpha 330 72
954 1490110 Homo Sapiensinterferon-omega 1 330 72
955 gi9844580Homo SapiensdJ1153D9.4 (novel protein)623 84
955 gi9844579Homo SapiensdJ1153D9.3 (novel protein)450 97
955 gi 15928971Homo SapiensSimilar to neuronal 430 90
thread protein
956 gi12804321Homo Sapiensperoxisomal short-chain685 100
alcohol
dehydrogenase
956 gi19113668Homo SapiensNADP-dependent retinol 878 100
dehydrogenase
short isoform
956 gil 1559412Homo SapiensNADPH-dependent retinol587 100
dehydrogenase/reductase
957 gi12718818Mus musculussulfhydryl oxidase 496 49
957 gi12718820Rattus sulfhydryl oxidase 489 47
norvegicus
957 gi12483919Rattus FAD-dependent sulfhydryl489 47
norvegicusoxidase-2
958 112958660Homo Sapiensacid phosphatase 2252 100
958 gi12958663Homo Sapiensacid phosphatase variant1285 99
3
958 gi52871 Mus musculuslysosomal acid phosphatase837 45
959 gi28966 Homo Sapiensalpha 1-antitrypsin 1703 100
959 gi6855601Homo SapiensPR00684 1703 100
959 111493443Homo SapiensPR02209 1703 100
960 gi28966 Homo Sapiensalpha 1-antitrypsin 1080 100
960 gi11493443Homo SapiensPR02209 1080 100
960 gi177829 Homo Sapiensalpha-1-antitrypsin 1080 100
961 gi28966 Homo Sapiensalpha 1-antitrypsin 1239 100
961 111493443Homo SapiensPR02209 1239 100
961 gi177829 Homo Sapiensalpha-1-antitrypsin 1239 100
962 gi28966 Homo Sapiensalpha 1-antitrypsin 1574 93
962 gi11493443Homo SapiensPR02209 1574 93
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
962 gi177829 Homo Sapiensalpha-1-antitrypsin 1574 93
963 gi6706993Streptomycesmethyltransferase 83 26
coelicolor
A3(2)
963 gi7303904DrosophilaCG13954-PA 85 53
melanogaster
964 gi2632092Pongo fertilin alpha protein 4128 92
pygmaeus
964 gi794073 Macaca fertilin alpha-I 3136 74
fascicularis
964 gi1841702Macaca fertilin alpha-I isoform3136 74
fascicularis
965 gi4107229Homo Sapienslipophilin A 454 1
00
_
965 gi4107231Homo Sapienslipophilin B 267 __
60
965 gi17887359~ryctolaguslipophilin AL2 248 54
cuniculus
966 gi3335100Homo sapiensCD39L3 2816 100
966 gi13817037Homo SapiensE-type ATPase 2812 99
966 gi20988653Homo SapiensSimilar to ectonucleoside2413 99
triphosphate
diphosphohydrolase 3
967 gi6942096Mus musculusCBLN3 936 93
967 gi180251 Homo Sapiensprecerebellin 549 57
967 gi5702371Mus musculusprecerebellin-1 542 56
968 gi17390957Mus musculusSimilar to RII~EN cDNA 129 32
2010001E11
gene
968 gi16410838Listeria similar to multidrug-efflux95 27
monocytogenestransporter
968 gi4914624Listeria multidrug resistance 95 27
monocytogenestransporter
969 gi17390957Mus musculusSimilar to RII~EN cDNA 191 26
2010001E11
gene
969 gi2828808Bacillus glucose transporter 100 23
subtilis
969 gi14~02314~8Z'~Icsorhi~obiumprobable fosmidomyoin 112 25
loti resistance protein
970 ' 13161123Homo Sapienstranscript Y 10 151 54
970 gi4545317Acipenser immunoglobulin light 160 25
ruthenus chain precursor
970 gi9937599Salmo truttaMHC class I heavy chain160 31
971 gi4160197Homo SapiensdJ327J16.2 (supported 2515 99
by GENSCAN
and GENEWISE)
971 gi2253263Rattus neuronal pentraxin receptor2238 89
norvegicus
971 gi12744624Mus musculusneuronal pentraxin receptor2212 88
972 gi4760782Mus musculusTen-m4 4188 96
972 gi3170615Mus musculusDOC4 4166 96
972 gi5307785Danio rerioten-m4 3537 78
973 gi14714932Homo SapiensSimilar to nuclear factor3770 100
(erythroid-
derived 2)-like 1
973 gi473090 Mus musculusNFE2-related factor 3644 96
1
973 gi3978250Mus musculusNrfl splice variant 3280 96
D
974 gi7716100Rattus selective LIM binding 8413 95
norve 'cusfactor
974 gi17044301Leishmaniapossible LIM-binding 2139 36
maj or factor
974 gi10440379Homo sapiensFLJ00025 protein 135 25
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
975 gi20799661Mus musculusmucolipin-2 1593 72
975 gi20987535Mus musculusRIKEN cDNA 3300002004 1590 71
gene
975 gi19072756Mus musculusmucolipin-3 1136 51
976 gi20799661Mus musculusmucolipin-2 2394 83
976 gi20987535Mus musculusRIKEN cDNA 3300002004 2391 82
gene
976 119072754Homo Sapiensmucolipin-3 1674 59
977 gi403020 Mus musculusEn-2/lacZ fusion protein988 96
977 gi14193747Mus musculuszinc finger 142 258 24
977 gi1510147Homo sapienssimilar to Human zinc 223 20
finger
protein(ZNF 142)
978 gi10581238HalobacteriumVng1783h 54 46
sp. NRC-1
978 gi19699294ArabidopsisAT3g48750/T21J18 20 73 30
thaliana
979 '7959724 Homo SapiensPR00929 63 30
979 gi13540242Anopheles NADH dehydrogenase subunit62 31
stephensi 5
979 gi20904847Methanosarcina8-oxoguanine DNA glycosylase64 40
mazei Goel
980 gi5281519Homo SapiensHTRA serine protease 2164 100
980 gi1513059Homo Sapiensserin protease with 2164 100
IGF-binding motif
980 gi1621244Homo Sapiensnovel serine protease, 2164 100
PRSS11
981 gi7008025Callithrixprochymosin 832 68
jacchus
981 gi19851892Bos tauruschymosin precursor 515 77
981 gi162860 Bos tauruspreprochymosin b 752 62
982 gi18461371Rattus sulfatase FP 276 68
norveaicus
982 gi21961489Mus musculusSimilar to sulfatase 276 68
FP
982 gi15430244Coturnix N-acetylglucosamine-6-sulfatase263 68
coturnix
983 gi3043872Lactococcustransmembrane protein 69 32
lactic Tmp3
983 gi17428881Ralstonia CONSERVED HYPOTHETICAL 62 34
solanacearumPROTEIN
983 gi433707 Zea mat's prolin rich protein 63 48
984 gi6013463Bothrops carboxypeptidase homolog826 46
jararaca
984 gi9558448Mus musculuscarboxypeptidase R 812 45
984 gi7416967Mus musculusthrombin-activatable 812 45
fibrinolysis inhibitor
985 gi6013463Bothrops carboxypeptidase homolog826 46
jararaca
985 19558448 Mus musculuscarboxypeptidase R 812 45
985 gi7416967Mus musculusthrombin-activatable 812 45
fibrinolysis inhibitor
986 gi11545707Homo SapiensISCL12 845 100
986 gi20381021Mus musculusRIKEN cDNA 2310020H20 807 96
gene
986 gi11545705Homo SapiensISCUl 663 99
987 gi12314022Homo SapiensdJ553F4.4 (Novel protein881 89
similar to
Drosophila CG8055 protein)
987 gi22417143Homo sapiensCGI-301 protein 853 100
987 gi13182765Homo SapiensCDA04 560 60
988 gi52959 Mus musculusprecursor polypeptide 146 34
(AA -26 to 108)
988 gi198922 Mus musculuslymphocyte differentiation145 34
antigen
988 gi198926 Mus musculusLy-6A.2 alloantigen 145 34
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
990 gi15990480Homo SapiensSimilar to AE-binding 1570 100
protein 2
990 gi4106464Mus musculusAE-1 bindin protein 1555 98
AEBP2
990 gi21595036Mus musculusAE binding protein 2 1555 98
991 gi23903 Homo Sapiens63kDa protein kinase 2897 99
991 gi204058 Rattus extracellular signal-related1499 62
norvegicuskinase 3
991 gi16306437Homo SapiensERK-3 1492 62
992 gi17016967Homo SapiensNUANCE 3403 90
992 gi17861384Homo Sapiensnesprin-2 gamma 3403 90
992 '21748548Homo SapiensFLJ00347 protein 3403 90
993 120070711Homo Sapienssimilar to RIKEN cDNA 997 100
2310044D20
993 gi18204756Mus musculusSimilar to RII~EN cDNA 626 68
2310044D20
gene
993 gi7304139DrosophilaCG12159-PA 111 28
melanogaster
994 gi14278927Mus musculusgliacolin 866 68
994 gi10566471Mus musculusGliacolin 866 68
994 gi3747099Mus musculusClq-related factor 734 67
995 gi20987689Homo SapiensSimilar to allantoicase1838 99
995 gi14718648Homo Sapiensallantoicase 1633 99
995 gi9255889Mus musculusallantoicase 1476 77
997 gi2522208Homo SapiensRas-GRF2 6407 99
997 gi5882290Homo sapiensRas guanine nucleotide 6401 99
exchange factor 2
997 gi57665 Rattus P140 RAS-GRF 4121 65
rattus
998 gi22038159Homo Sapiensziziminl 8544 100
998 '14597976Homo Sapienshuman CLASP-4. 3533 56
998 gi550420 Rattus trg 2842 87
norvegicus
999 gi 17861850DrosophilaGM03763p 334 70
melanogaster
999 gi17862036DrosophilaLD05823p 265 47
melanogaster
999 '10178624.Mus znusculusSETA bindin protein 215 4.5
1; SB1
1000gi21594273Homo SapiensSAC2 suppresser of actin3626 100
mutations 2-
like (yeast)
1000gi14041697Homo SapiensdJ1033B10.5.1 (SAC2 3587 99
(suppresser of
actin mutations 2, yeast,
homology-like
(AREl), isoform 1)
1000gi3850063Rattus ARE1 3576 98
norvegicus
1001gi1438534Rattus rA9 4002 61
norvegicus
1001gi1438532Rattus rAl 430 36
norvegicus
1001gi9438033Homo sapiensser/arg-rich pre-mRNA 407 35
splicing factor
SR-A 1
1002gi1438534Rattus rA9 4002 61
norvegicus
1002gi9438033Homo Sapiensser/arg-rich pre-mRNA 407 35
splicing factor
SR-A1
1002gi10440402Homo SapiensFLJ00034 protein 407 35
1003gi1675220CricetulusSREBP cleavage activating6200 92
griseus protein
1003gi20378357DrosophilaER- of i escort protein810 39
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
melanogaster
1003gi10728147DrosophilaCG8356-PA 810 39
melanogaster
1004112652851Homo Sapienspotassium channel modulatory1987 100
factor
1004'4838557 Mus musculusDEBT-91 1453 96
1004gi16768790DrosophilaLD03515p 876 63
melanogaster
1005gi7270532ArabidopsisDNA-directed RNA polymerase173 29
thaliana (EC
2.7.7.6) II largest
chain
1005gi16505 ArabidopsisRNA polymerase II 173 29
thaliana
1005gi16494 ArabidopsisDNA-directed RNA polymerase173 29
thaliana
1006gi11875318Mus musculussynaptotagmin XIII 2004 89
1006gi21410154Mus musculussynaptotagmin 13 2004 89
1006gi11119239Rattus synaptotagmin 13 2000 89
norvegicus
1007gi3800881Homo SapiensRanBP7/importin 7 5447 100
1007gi11342591Mus musculusRanBP7/importin 7 5418 99
1007gi11544639Homo Sapiensimportin7 5307 100
1008gi5578958Homo SapiensdJ475B7.2 (novel protein)3770 99
1008gi18676522Homo SapiensFLJ00158 protein 1512 100
1008gi21595156Mus musculusSimilar to RII~EN cDNA 1151 71
5830482623
gene
1009gi4406393Bos taurusdifferentiation enhancing4699 95
factor 1
1009gi4063614Mus musculusADP-ribosylation factor-directed4694 94
GTPase
activating protein isoform
a
1009gi4063616Mus musculusADP-ribosylation factor-directed3186 79
GTPase
activating protein isofonn
b
1010gi16411927Listeria 1mo2439 57 52
monocytogenes
1010gi16415055Listeria 1in2533 61 ~7
innocua
1010gi2983786f~quife~ glucose-1-phosphate 70 39
aeolicus thymidylyltransferase
1011gi9280405Homo Sapiensadlican 1631 47
1011gi13872813Homo Sapienstibulin-6 502. 28
1011gi3328186Caenorhabditishemicentin precursor 539 27
elegans
1012gi4001698Sus scrofamat-8 67 30
1012gi2622724Methanothermoconserved protein 82 29
bacter
thermautotrophi
cus str.
Delta
H
1012gi498166 Mus musculuszona-pellucida-bindin 85 27
protein (sp38)
1013gi 17511816Homo SapiensSimilar to RIICEN cDNA 1468 99
1110032022
gene
1013gi7211438Homo Sapiensgolgin-67 100 30
1013gi6003208Human p17 protein 84 29
immunodeficien
cy virus
type 1
1014gi 17511816Homo SapiensSimilar to RIKEN cDNA 878 100
1110032022
gene
1014gi6003208Human p17 protein 84 29
immunodeficien
cy virus
type 1
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1014gi21957065Yersinia uroporphyrinogen III 90 34
pestis methylase
I~IM
1015gi2246401Homo Sapienscentrin 842 100
1015gi13529248Homo Sapienscentrin, EF-hand protein,839 99
3 (CDC31 yeast
homology
1015gi2246424Mus musculuscentrin 832 98
1016gi17428765Ralstonia CONSERVED HYPOTHETICAL 530 43
solanacearumPROTEIN
1016gi15155946AgrobacteriumAGR C_1725p , 379 41
tumefaciens
str.
C58 (Cereon)
1016gi15073913SinorhizobiumCONSERVED HYPOTHETICAL 372 39
meliloti PROTEIN
1017gi17428765Ralstonia CONSERVED HYPOTHETICAL 381 43
solanacearumPROTEIN
1017gi15073913SinorhizobiumCONSERVED HYPOTHETICAL 367 48
meliloti PROTEIN
1017gi12543118CorynebacteriuRXC01693 265 30
m glutamicum
1018gi6693701Homo Sapiensmelanopsin 2234 91
1018gi21928729Homo Sapiensseven transmembrane 2190 99
helix receptor
1018gi6693703Mus musculusmelanopsin 1735 73
1019gi439296 Homo Sapiensgarp 822 37
1019gi6572272Homo SapiensdJ756G23.1 (novel Leucine243 34
Rich Protein)
1019gi19344010Homo Sapiensinsulin-like growth 293 29
factor binding protein,
acid labile subunit
1020'15706421Homo Sapiensmiddle-chain aryl-CoA 1346 99
synthetasel
1020gi15487302Homo Sapiensmedium-chain acyl-CoA 1346 99
synthetase
1020gi5019275Bos taurusxenobiotic/medium-chain1088 78
fatty acid:CoA
ligase form XL-III
1021gi6650766Homo SapiensPDZ domain-containing 6216 100
guanine
nucleotide exchan a
factor I
1021gi20386206Homo sapienSPDT domain-containing 5822 98
guanine
nucleotide exchange
factor PDT-GEF2
1021gi18874700Homo sapiensRapl guanine nucleotide-exchange5803 98
factor
PDT-GEF2B
1022gi20386206Homo sapiensPDT domain-containing 5942 100
guanine
nucleotide exchange
factor PDZ-GEF2
1022gi18874700Homo SapiensRapl guanine nucleotide-exchange5923 99
factor
PDZ-GEF2B
1022gi18874698Homo SapiensRapl guanine nucleotide-exchange5923 99
factor
PDZ-GEF2A
1023gi13810306Homo Sapienstransmembrane protein 268 37
7
1023gi18250724Mus musculustransmembrane protein 264 37
7
1023gi20270907OncorhynchusVHSV-induced protein-5 243 33
myleiss
1024gi21779869Homo SapiensIL-17RE 2896 100
1024gi21779866Mus musculusIL-17RE 1394 74
1024gi21779857Homo SapiensIL-17RC 246 29
1025gi21779869Homo SapiensIL-17RE 2928 100
1025gi21779866Mus musculusIL-17RE 1388 75
1025gi21779857Homo SapiensIL-17RC 246 29
1026gi14150450Rattus UDP-GaINAc:polypeptide 1352 93
norvegicusN-
acetylgalactosaminyltransferase
T9
1026gi16769916DrosophilaSD10722p 473 38
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
melanogaster
1026gi21627105DrosophilaCG30463-PA 417 38
melanogaster
1027gi15217067Homo Sapiensstem cell factor isoform1013 95
1
10271337934 Homo Sapiensstem cell factor 1013 95
1027gi1827477Felis catusstem cell factor 893 84
1028gi1377894Homo SapiensOB-cadherin-1 1478 64
1028gi1377895Homo SapiensOB-cadherin-2 1478 64
1028gi506404 Homo Sapienscadherin-11 1474 63
1029gi1377894Homo SapiensOB-cadherin-1 1628 56
1029gi1377895Homo SapiensOB-cadherin-2 1628 56
1029gi506404 Homo Sapienscadherin-11 1623 56
1030gi1398903Mus musculusCa2+ dependent activator6314 90
protein for
secretion
1030gi577428 Rattus Ca2+-dependent activator5003 96
norvegicusprotein;
calcium-dependent actin-binding
protein
1030gi6980012Drosophilasecretion calcium-dependent3540 60
melano activator
aster protein
1031gi217705 Sus scrofadipeptidase precursor 781 51
1031gi2102 Susscrofa dipeptidase 781 51
1031gi8248922Homo Sapiensrenal dipeptidase; RDP 762 50
1032gi18073362Homo Sapienscystine/glutamate transporter2552 100
1032gi11493652Homo Sapienscalcium channel blocker2552 100
resistance
protein CCBRl
1032gi 13924720Homo Sapienscystine/glutamate transporter2562 100
xCT
1033gi17028348Homo SapiensSimilar to methylenetetrahydrofolate3748 100
dehydrogenase (NADP+
dependent),
methenyltetrahydrofolate
cyclohydrolase,
formyltetrahydrofolate
synthetase
1033120987924Mus musculusSimilar to DI~FZPS86G15173473 92
protein
1033gi307178 Homo SapiensMDMCSF (EC 1.5.1.5; 2839 62
EC 3.5.4.9; EC
6.3.4.3)
1034gi632676 Saccharomyces~1r410v,~p 598 44
cerevisiae
1034gi4070 Saccharomycesnufl 120 20
cerevisiae
1034gi312175 SaccharomycesSPC110/NUF1 120 20
cerevisiae
1035gi11066463Rattus I2hoGEF glutamate transport5589 80
norvegicusmodulator
GTRAP48
1035' 19387126Mus musculusanine nucleotide exchange1794 37
factor
1035'7110160 Homo Sapiensanine nucleotide exchange1792 37
factor
1036gi2921821Rattus cytochrome P450 IIE1 68 28
norvegicus
1036gi8515399Human attachment glycoprotein64 29
respiratoryG
syncytial
virus
1036gi5901834DrosophilaBcDNA.GH09358 95 23
melanogaster
1037gi17128288synthetic Primer 1 1689 100
construct
1037'20269957Sus scrofaphospholipase C delta 1469 85
4
1037121307610Mus musculusphospholipase C delta 1327 77
4
1038gi6978948Homo Sapiensvaccinia related kinase76 24
3
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1038gi349667 Carnobacteriumcarnobacteriocin A 60 41
piscicola
1038gi406315 Carnobacteriumpiscicolin 61 60 41
piscicola
1039gi4159884Homo Sapienssimilar to mouse olfactory1597 99
receptor 13;
similar to P34984 (PID:g464305)
1039gi9368991Homo SapiensdJ1005H11.1 (7 TRANSMEMBRANE1410 100
RECEPTOR (RHODOPSIN
FAMILY)
(OLFACTORY RECEPTOR
LIKE)
PROTEIN))
1039gi18480186Mus musculusolfactory receptor MOR261-61323 81
1040gi311626 Homo Sapiensthrombospondin-4 4787 99
1040gi3860231Mus musculusthrombospondin-4 4557 93
1040gi929835 Rattus thrombospondin-4 4547 93
norvegicus
1041gi14043083Homo Sapienssperm associated antigen660 100
9
1041gi3116015Homo Sapienssperm specific protein _ 98
273
1041gi10801148Mus musculusJNK/SAl'K-associated 98 41
protein 1
1042gi21654741Homo Sapienspeptide/histidine trans1746 98
orter
1042gi2208839Rattus peptide/histidine transporter1469 79
norvegicus
1042gi16740719Mus musculusSimilar to peptide transporter1453 83
3
1043gi21392228DrosophilaRH61354p 1221 41
melano
aster
1043gi19353264Homo sapiensSimilar to dishevelled 2224 65
associated activator
of morphogenesis 2
1043gi2947238Homo Sapiensdiaphanous 1 717 32
1044gi 15929979Homo SapiensSimilar to zinc finger 2476 100
protein 345
1044' 18643896Homo Sapienszinc finger protein 1656 53
1044gi1020145Homo SapiensDNA binding protein 1656 53
1045gi12655913Homo sapienssprouty-4A 386 98
1045gi4850326Mus musculussprouty-4 323 81
1045gi5917720Mus musculussprouty 4 323 81
1046gi4539525Homo sapiensNAALADase II protein 3881 100
1046gi3211746Sus scrofafolylpoly-gamma-glutamate2824 70
carboxypeptidase
1046gi2897946Homo Sapiensprostate-specific membrane2787 69
antigen
1047gi5420389Leishmaniaproteophosphoglycan 139 23
maj or
1047gi915207 Sus scrofagastric mucin 123 22
1047gi13592175Leishmaniappg3 125 23
major
1048gi5918167Homo Sapiensplexin-B1/SEP receptor 2104 54
1048gi6010211Homo Sapienssemaphorin receptor 2103 54
1048gi1655432Mus musculusplexin 2 1517 30
1049gi15990515Homo SapiensSimilar to RIKEN cDNA 3035 100
0610020I02
gene
1049gi18380977Mus musculusRIKEN cDNA 0610020I02 2792 92
gene
1049gi2384732Rattus NAC-1 protein 1269 57
norve 'cus
1050gi15088540Homo Sapienssterolin-2 3127 99
1050gi11692802Homo SapiensABCG8 3123 99
1050gi15146444Homo Sapienssterolin-2 3120 99
1051gi12652851Homo Sapienspotassium channel modulatory1987 100
~ ~ ~ factor
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TABLE 2 A
SEQ Hit H) Species Description S Percentage
ID scoreidentit
1051gi4838557Mus musculusDEBT-91 145396
1051gi16768790DrosophilaLD03515p 876 63
melanogaster
1052gi33730 Homo Sapiensimmuno lobulin lambda 716 71
light chain
1052gi33395 Homo Sapienslambda-chain precursor 703 70
(AA -20 to 215)
1052gi33744 Homo Sapiensimmuno lobulin lambda 697 68
light chain
1053gi21388773Homo Sapiensla~ingle-containing protein1552100
1053gi21623530Homo Sapienskringle-containing transmembrane123899
protein
1053gi21388775Homo Sapienskringle-containing protein1241100
1054gi14495324Homo SapiensCMRF35A 421 48
1054gi18490143Homo SapiensCMRF35 leukocyte immunoglobulin-like421 48
receptor
1054gi396170 Homo SapiensCMRF-35 antigen 421 48
1055'4468256 Homo SapiensMHC class I antigen 1974100
1055gi32139 Homo SapiensHLA-Al 1E protein precursor191297
(AA -24 to
341)
1055gi487909 Homo sapiensHLA-Al l antigen Al 1.1 191297
1056gi21667214Homo Sapiensbactericidal/permeability-increasing741 100
protein-like 3
1056gi57732 Rattus potential li and-binding215 35
rattus protein
1056gi118'77276Homo SapiensdJ726C3.5 (ortholog of 176 32
potential
ligand binding protein
RY2G5 (Rat))
1057gi21667214Homo Sapiensbactericidal/permeability-increasing222699
protein-like 3
1057gi57732 Rattus potential ligand-bindin 579 32
rattus protein
1057gi11877276Homo SapiensdJ726C3.5 (ortholog of 540 31
potential
li and bindin protein
RY2G5 (Rat))
1058gi21667214Homo Sapiensbactericidal/permeability-increasing191999
protein-like 3
1058157732 Rattus potential ligand-bindin 485 33
rattus protein
1058gi11877276Homo SapiensdJ726C3.5 (ortholog of 447 31
potential
ligand binding protein
RY2G5 (Rat))
1059gi21667214=Homo Sapiensbactericidal/permeability-increasing184=2100
protein-like 3
1059gi57732 Rattus potential ligand-binding485 33
rattus protein
1059gi11877276Homo SapiensdJ726C3.5 (ortholog of 447 31
potential
ligand binding protein
RY2G5 (Rat))
1060gi23911 Homo Sapienspolypeptide 7B2 precursor1148100
1060'7718079 Homo Sapiensneuroendocrine protein 1148100
7B2
1060gi13529158Homo Sapienssecretory granule, neuroendocrine113199
protein
1 (7B2 protein)
1061gi18698601Homo SapiensSmith-Magenis syndrome 2325100
chromosome
region candidate 7 protein
1061gi15073752SinorhizobiumHYPOTHETICAL TRANSMEMBRANE90 29
meliloti SIGNAL PEPTIDE PRQTEIN
1061gi13623063Streptococcusheat shock protein - 70 32
pyogenes cochaperonin
M1
GAS
1062gi4128041Homo Sapiensclaudin-9 protein 1116100
1062gi4325296Mus musculusclaudin-9 107895
1062gi14286272Homo Sapiensclaudin 6 826 71
1063gi14286258Homo Sapiensribosomal protein L29 432 65
1063gi1215742Homo SapiensHIP 432 65
~ gi793843 Homo sapiensribosomal protein L29 432 65
1063~ ~ ~
~
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1064gi6601555Rattus glutamate receptor interacting3560 86
norvegicusprotein 2
1064gi3639077Rattus AMPA receptor binding 2743 88
norvegicusprotein
1064gi1890856Rattus AMPA receptor interacting1925 59
norvegicusprotein GRIP
1065gi3288852Homo Sapiensdisabled-1 2865 99
1065gi1771282Mus musculusmDab555 protein 2797 96
1065gi22095317Gallus disabled-1 2630 90
gallus
1066gi3002527Homo Sapiensneuronal thread protein164 86
AD7c-NTP
1066gi4336401Homo Sapiensbeta glucuronidase isoform127 72
d
1066gi4336402Homo Sapiensbeta glucuronidase isoform127 72
c
1067115430703Homo Sapienstestis specific serinelthreonine1858 99
kinase 2
1067gi2738898Mus musculusprotein kinase 1686 89
1067gi15283993Homo Sapienstestis-specific serine/threonine1230 77
kinase 1
1068gi13543568Homo sapiensprostaglandin D2 synthase977 96
(2lkD, brain)
1068gi12963879Homo Sapiensprostaglandin D synthase977 96
1068gi189772 Homo Sapiensprostaglandin D2 synthase977 96
1069gi13279311Homo SapiensSimilar to RIKEN cDNA 1416 96
1500017E18
gene
1069gi14336718Homo Sapienssimilar to HAGH 1157 100
1069gi20988885Mus musculusRIKEN cDNA 1500017E18 1151 79
gene
1070gi13397835Homo sapiensannexin A13 isoform 1795 99
b
1070gi757784 Canis familiarisannexin 2~IIIb 1621 89
1070gi21218387~ryctolagusannexin XIIIb 1589 88
cuniculus
1071gi21707908Homo Sapienssolute carrier family 3129 98
6 (neurotransmitter
transporter, GABA),
member 1
1071gi31658 Homo SapiensGABA transporter 3114 98
1071gi204222 Rattus GABA transporter protein3097 96
norvegicus
1072gi7160975Homo Sapiensvoltage-gated sodium 834 100
channel beta-3
subunit
1072gi7161889Rattus voltage-gated sodium 823 98
norvegicuschannel beta-3
subunit
1072gi14165176Rattus sodium channel beta 823 98
norvegicus3 subunit
1074gi18676470Homo SapiensFLJ00132 protein 2515 99
1074gi21430928DrosophilaSD27341p 324 38
melanogaster
1074gi20197056Arabidopsisexpressed protein 206 29
thaliana
1075gi452751 Gallus Gal beta 1,4 GIcNAc 949 54
gallus alpha 2,6-
sialyltransferase
1075gi2295223unidentifiedGALACTOSYLTRANSFERASE- 856 48
SIALYLTRANSFERASE HYBRID
PROTEIN
1075gi29434 Homo Sapiensbeta-galactoside alpha-2,6-856 48
sialyltransferase
1076gi13344997Homo SapiensCat Eye Syndrome critical2223 100
region protein
isoform 2
1076gi13344995Homo SapiensCat Eye Syndrome critical2002 99
region protein
isoform 1
1076gi15928451Mus musculusSimilar to cat eye syndrome1649 76
chromosome
re ion, candidate 5
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1077gi13344997Homo SapiensCat Eye Syndrome critical1662 96
region protein
isoform 2
1077gi13344995Homo SapiensCat Eye Syndrome critical1662 96
region protein
isoform 1
1077gi15928451Mus musculusSimilar to cat eye syndrome1294 75
chromosome
region, candidate 5
1078i 177870 Homo Sapiensalpha-2-macro lobulin 2714 39
precursor
10781579592 Homo Sapiensalpha 2-macroglobulin 2708 39
690-730
10781579594 Homo Sapiensalpha 2-macroglobulin 2700 39
690-740
1079gi671864 Gallus ovomacroglobulin, ovostatin1300 34
gallus
1079gi579594 Homo Sapiensalpha 2-macroglobulin 1297 35
690-740
1079gi177870 Homo Sapiensalpha-2-macroglobulin 1296 35
precursor
1080gi671865 Gallus ovomacroglobulin, ovostatin806 32
gallus
1080gi177870 Homo Sapiensalpha-2-macroglobulinprecursor769 31
1080gi579592 Homo Sapiensalpha 2-macroglobulin 769 31
690-730
1081gi177870 Homo Sapiensalpha-2-macroglobulin 2732 40
precursor
1081gi579592 Homo Sapiensalpha 2-macroglobulin 2726 40
690-730
1081gi579594 Homo Sapiensalpha 2-macroglobulin 2718 39
690-740
10821579594 Homo Sapiensalpha 2-macroglobulin 1297 35
690-740
1082gi177870 Homo Sapiensalpha-2-macro lobulin 1296 35
precursor
1082gi579592 Homo Sapiensalpha 2-macroglobulin 1296 35
690-730
1083gi404389 Mus sp. carboxylesterase; Es-male2006 66
1083gi213101 Anas thioesterase B 1261 46
platyrhynchos
1083gi2058318Homo sapienScarboxylesterase 1253 47
1084gi207286 Rattus TGF-beta masking protein8731 89
norvegicuslarge subunit
1084gi3493176Mus musculuslatent TGF beta binding8640 88
protein
1084gi19909128Homo Sapienstransforming growth 7763 99
factor-beta binding
protein-1 S
1085gi17985371Homo SapiensI3 binding protein 861 100
1085gi21961229Homo SapiensBkI3 binding protein 861 100
1085gi184=668081-Iomo cervical cancer 1 proto-oncogene-binding853 99
sapienS pr~tein I~G19
1086gi222833 Gallus M-protein 2953 42
gallus
1086gi407097 Homo Sapiens165kD protein 29 42
33
1086gi2950347Mus musculusM-protein _ 42
2931
1087gi12655165Homo Sapienszinc linger protein 696 65
256
1087gi4894364Homo Sapienszinc finger protein 696 65
3
1087gi21327296Homo Sapienszinc finger protein 495 46
382
1088gi2689441Homo SapiensF18547_1 188 37
1088gi1613848Homo Sapienszinc finger protein 316 49
zfp6
1088121327296Homo Sapienszinc finger protein 203 38
382
1089112655460Homo Sapienskeratin associated protein929 75
4.12
1089gi13278825Homo SapiensSimilar to RII~EN cDNA 929 75
1110054P19
gene
1089gi12655464Homo Sapienskeratin associated protein900 83
4.15
1090gi12655460Homo Sapienskeratin associated protein403 85
4.12
1090gi13278825Homo SapiensSimilar to RIKEN cDNA 403 85
1110054P19
gene
1090gi12655442Homo Sapienskeratin associated protein397 84
4.2
1091112655464Homo Sapienskeratin associated rotein1260 100
4.15
1091gi12655452Homo Sapienskeratin associated protein1222 90
4.7
1091gi12655460Homo Sapienskeratin associated protein1156 88
4.12
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1092gi15722084Homo SapiensbA304I5.1 (novel lipase)1991 100
1092gi21594466Mus musculusRIKEN cDNA 4632427023 1928 87
gene
1092gi460143 Homo Sapienslysosomal acid lipase/cholesteryl1290 60
ester
hydrolase
1093gi21594466Mus musculusRIKEN cDNA 4632427023 1957 88
gene
1093gi15722084Homo SapiensbA304I5.1 (novel lipase)1935 100
1093gi460143 Homo Sapienslysosomal acid lipase/cholesteryl1290 60
ester
hydrolase
1094'8118040 Homo sa orphan G-protein coupled1804 99
iens receptor
1094gi8118052Mus musculusorphan G-protein coupled1306 82
receptor
1094gi13177796Homo sapiensretinoic acid induced 728 45
3
1095gi18129609Homo sapiensdiacylglycerol acyltransferase600 49
2
1095gi15099951Mus musculusdiacylglycerol acyltransferase599 49
2
1095gi17426446Homo SapiensbA351I~23.5 (novel protein)572 54
1096gi17225337Homo Sapiensdendritic lectin 1134 95
1096gi17224598Homo Sapiensblood dendritic cell 1134 95
antigen 2 protein
1096gi17225339Homo Sapiensdendritic lectin b isoform918 94
1097gi17225337Homo Sapiensdendritic lectin 1182 99
1097gi17224598Homo Sapiensblood dendritic cell 1182 99
antigen 2 protein
1097' 17225339Homo Sapiensdendritic lectin b isoform966 99
1098121929119Homo Sapiensseven transmembrane 1595 100
helix receptor
1098118479834Mus musculusolfactory receptor M~R144-11223 77
1098gi18480806Mus musculusolfactoryreceptor M~R143-11163 70
1099gi5911169Homo Sapienstransmembrane mucin 3049 99
12
1099gi19526645Homo Sapiensintestinal membrane 815 32
mucin MUC17
1099gi5911171Homo Sapiensmucin 11 684 4~7
1100gi37198 Homo SapiensTMl-CEA preprotein 455 34
1100gi179440 Homo Sapiensbiliary glycoprotein 455 34
I precursor
1100gi550031 Homo SapiensBGPc 455 34
1101gi6273399Homo Sapiensmelanoma-associated 4733 60
antigen MG50
1101gi1504040Homo sapienssimilar to D.melanogaster4733 60
peroxidasin(U11052)
1101gi531385 Drosophilaperoxidasin precursor 2013 39
melanogaster
1102gi6273399Homo Sapiensmelanoma-associated 4458 60
antigen MG50
1102gi1504040Homo Sapienssimilar to D.melanogaster4458 60
peroxidasin(Ul 1052)
1102gi531385 Drosophilaperoxidasin precursor 2013 39
melano
aster
1103gi7264653Mus musculusICiaa0575 2398 61
1103gi11611734Homo SapiensGREBla 513 46
1103gi915208 Sus scrofagastric mucin 128 30
1104gi20219008Chlamydomonacoiled-coil flagellar 682 36
s reinhardtiiprotein
1104gi16519041Drosophilaoccludin-like protein 203 23
melanogaster
1104gi3549261Dictyosteliuminteraptin 175 22
discoideum
1105gi12654511Homo SapiensATP-dependant interferon693 96
response
protein 1
1105gi17390689Homo SapiensATP-dependant interferon693 96
responsive
1105gi10862826Homo SapiensADIRl 689 95
1106gi15215375Homo SapiensRNA bindin motif protein325 72
12
1106gi21666372Homo Sapiensswan 325 72
~ ~
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1106gi19070194Homo SapiensSWAN 325 72
1107gi18157547Mus musculuspecanex-like 3 3262 97
1107gi6650377Mus musculuspecanex 1 2530 74
1107gi15076843Homo Sapienspecanex-like protein 2526 74
1
1108gi18157547Mus musculuspecanex-like 3 3138 97
1108gi6650377Mus musculuspecanex 1 2409 73
1108gi15076843Homo Sapienspecanex-like protein 2405 73
1
1109gi7770237Homo SapiensPR02822 233 59
1109gi21595759Homo Sapienssimilar to HC6 211 71
1109gi3002527Homo Sapiensneuronal thread protein209 67
AD7c-NTP
1110gi18159337PyrobaculumpaREP8 77 30
aerophilum
1110gi1658310Homo Sapiensleukocyte surface protein97 26
1110gi7638235Mus musculusimmunoglobulin heavy 77 25
chain variable
domain
1111gi4263743Homo Sapienssimilar to UNC-93; similar1575 100
to U89424
(PID:g3642687)
1111gi12043567Homo Sapiensunc-93 related protein 1571 99
1111' 17390915Mus musculusSimilar to unc93 (C.elegans)1372 87
homolog B
1113gi4153873Homo Sapienssimilar to weal-like 2810 100
protein kinase;
similar to P30291 (PID:g1351419)
1113gi644770 Xenopus WeelA kinase 1166 64
laevis
1113gi2827996Xenopus weal homolog 1166 64
laevis
1114gi6606119Dothidea DNA-dependent RNA polymerase81 32
insculpta II
RPB14~0
1114gi2796053Mus musculusT cell receptor beta 54~ 48
chain
1115gi20372871Clarkia cytosolic phosphoglucose56 28
similis isomerase
1116gi21708029Homo Sapienssimilar to Alu subfamily135 70
Sf~ sequence
contamination warnin
entry
1116gi11493409Homo SapiensPRO0898 129 59
1116gi6650818Homo sapiensPRO1992 110 70
1117gi13810898Rattus inhibin binding protein310 37
norvegicuslong isoform
1117gi2645890Homo SapiensIGSF1 326 40
1117gi2370143Homo Sapiensimmunoglobulin-like 326 40
domain-containing
1
1118gi13810898Rattus inhibin binding protein310 37
norvegicuslong isoform
1118gi2645890Homo SapiensIGSF1 312 38
1118gi2370143Homo Sapiensimmunoglobulin-like 312 38
domain-containing
1
1119gi21707128Homo SapiensRan binding protein 5047 99
11
1119gi20987296Mus musculusSimilar to Ran bindingprotein4898 96
11
1119gi17862636DrosophilaLD41918p 1191 38
melano
aster
1120gi18652832Homo SapiensASPP1 protein 5703 99
1120gi16197705Homo SapiensASPP2 protein 1556 42
1120gi1399805Homo SapiensBbp/53BI'2 1556 42
1121gi18448478Aotus chorionic gonadotropin 47 59
trivirgatusbeta subunit
1121gi5670272Human Kl glycoprotein 67 38
herpesvirus
8
1121gi9886851Human Kl protein 63 36
herpesvirus
8
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TART,F 2 A
SEQ Hit H) Species Description S Percentage
ID scoreidenti
1122gi2598461Homo SapiensdJ408N23.1 (suppression 188797
of
tumorigenicity 13 (colon
carcinoma)
(Hsp70-interacting protein)
(Progesterone
receptor associated P48
protein))
1122gi904032 Homo Sapiensp48 186996
1122gi21218374Homo SapiensFAM10A5 181493
112318927428 Homo Sapiensotoraplin 676 100
1123i 12619173Homo Sapiensmelanoma inhibitory activity676 100
like protein
1123gi11323317Homo SapiensdJ705D16.2 (Otoraplin) 676 100
1124gi12034719Mus musculusankyrin-like protein 462 46
1124gi13469729Homo Sapiensbreast cancer antigen 448 50
NY-BR-1
1124gi21618588Homo Sapienstestis-specific ankyrin 381 47
motif containing
protein
1125gi13469729Homo Sapiensbreast cancer antigen 364 51
NY-BR-1
1125gi12034719Mus musculusankyrin-like protein 379 46
1125gi21618588Homo sapienstestis-specific ankyrin 345 49
motif containing
protein
1126gi7770139Homo SapiensPRO1722 263 60
1126gi 11493483Homo SapiensPRO2550 263 67
1126gi8572229Homo Sapiensubiquitous TPR-motif 249 61
protein Y isoform
1127gi6907090_ Similar to Oryza sativa 86 35
Oryza sativaroot-specific
(japonica RCc3 mRNA. (L27208)
cultivar-group)
1127gi5902450Cercopithecineglycoprotin G 58 41
herpesvirus
1
1127gi12750734Homo SapiensL-type voltage-dependent56 48
calcium
channel
1128gi16878260Homo sapiensSimilar to angiotensin 726 100
II, type I receptor-
associated protein
1128gi16588454Homo SapiensAGTRAP protein 705 95
1128gi9621816Homo SapiensATRAP 705 95
1129gi 17986216Homo sapienscell recognition molecule186498
CASPR3
1129gi12330704Mus musculuscell reco iition molecule137671
CASPR4
1129gi21961652Mus musculuscell recognition protein137671
CASPR4
1130gi17986216Homo Sapienscell reco ition molecule681299
CASPR3
1130gi18390059Homo Sapienscell recognition protein475470
CASPR4
1130121961652Mus musculuscell recognition protein472468
CASPR4
1131gi21552969Mus musculusVVilliams-Beuren syndrome310097
critical region
ene 17
1131gi10336504~Homo sapiensUDP-GaINAc: polypeptide 202061
N-
acetylgalactosaminyltransferase
1131gi11041469Macaca UDP-GaINAc: polypeptide 191358
fascicularisN-
acetyl alactosaminyltransferase
1132gi13625176Homo Sapiensthrombospondin 586 46
1132gi14627121Homo sapiensdJ824F16.3 (novel protein544 46
similar to
mouse thrombospondin
type 1 domain
protein R-spondin)
1132gi4519541Mus musculusthrombospondin type 1 511 43
domain
1133gi5305333Mus musculusprotein kinase Myak-S 865 50
1133gi18314319MesocricetusMx-interacting protein 865 50
auratus kinase PKM
1133gi5815143Mus musculusnuclear body associated 865 50
kinase 2a
1134gi14022292Mesorhizobiumcell division protein 45 36
loti
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1134gi180143 Homo SapiensCD53 glycoprotein 45 53
_1134gi180141 Homo Sapienscell surface antigen 45 53
1135gi14571502Homo Sapienscalcium-promoted Ras 4174 99
inactivator
1135gi2822157Homo sapienssimilar to GTl'ase-activating3961 99
proteins;
35% similar to JC5047
(PID: 2136083)
1135gi4185294Homo SapiensrasGAP-activating-like 1898 49
protein
1136gi11527987Gallus immunoglobulin-like 97 30
gallus receptorCHIR-A
1136gi432214 Human envelope glycoprotein 43 39
immunodeiiciengp120
cy virus
type 1
1136gi15026993Homo sapiensMUCSAC protein 64 38
1137gi15128103Mus musculusnephronectin 2971 87
1137gi15430248Mus musculusnephronectin lon isoform2640 80
1137gi16040981Mus musculusPOEM 2374 87
1139gi7638247Homo Sapiensmesenchymal stem cell 595 100
protein DSCD75
1139gi17946258DrosophilaRE58349p 165 34
melanogaster
1139gi21464462DrosophilaRH58440p 158 36
melanogaster
1140gi21619491Homo Sapienssimilar to expressed 235 83
sequence AW049604
1140gi6572294Homo SapiensbA262A13.1 (novel protein)126 48
1140gi215692 Bacteriophagegop protein 87 28
P4
1141gi21619491Homo Sapienssimilar to expressed 454 82
sequence AW049604~
1141gi6572294Homo SapiensbA262A13.1 (novel protein)239 48
1141gi215692 I3acteriophagegop protein 84 33
P4
1142gi20306274Homo Sapienstesticular haploid expressed1487 80
gene
1142gi10443967HomosapiensTHEGprotein _ 80
1487
1142gi7416134Homo Sapienstestis-specific gene 1487 80
1143gi21928259Homo Sapiensseven transmembrane 1023 100
helix receptor
1143gi18480746Mus musculusolfactory receptor M~R261-10864 84
1143~i18480744Mus musculusolfactory receptor M~R261-9858 82
1144gi21928655Homo sapiensseven transmembrane 1458 93
helix receptor
1144gi18480746Mus musculusolfactory receptor M~R261-101280 79
1144gi18480744Mus musculusolfactory receptor M~R261-91258 78
1145gi1707674Streptomyceselongation factor G 52 34
cinnamoneus
1146gi15779092Homo SapiensSimilar to syntaxin 1295 100
18
1146gi7707424Homo Sapienssyntaxin 18 1295 100
1146118203931Mus musculusSimilar to syntaxin 873 90
18
1147114573319Homo Sapiensinterleukin-1 HY2 812 99
1147gi18025344Homo Sapiensinterleuldn-1 receptor 809 99
antagonist-like
FILL theta
1147gi19068192Mus musculusIL-1F10 662 82
1148gi4103158Mus musculushair keratin acidic 1116 72
5; Ha5 keratin
1148gi3724107Homo Sapienskeratin, type I 1114 72
1148gi1668744Homo SapiensHHaS hair leeratin type1114 72
I intermediate
filament
1149gi19353375Mus musculusRII~EN cDNA 1110031I02 1417 84
gene
1149gi6166378Mus musculusgrowth suppressor 1L 141 30
1149gi15929776Homo Sapiensgrowth suppressor 1 137 41
1150gi13623421Homo SapiensSimilar to RIKEN cDNA 1336 90
5730589L02
gene
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TART.F 7 A
SEQ Hit ID Species Description S Percentage
ID scoreidentit
1150gi19484086Mus musculusRIKEN cDNA 5730589L02 128786
gene
1150gi1699265Homo Sapiensmalignant cell expression-enhanced392 57
gene/tumor progression-enhanced
gene
1151gi15419605Canis familiarismasticatory epithelia 120455
keratin 2p
1151gi14595019Homo Sapienskeratin 6 irs 117554
1151gi6092075Mus musculustype II cytokeratin 111651
1152gi11066090Homo Sapiensmatrix metalloprotease 138296
MMP-27
1152gi12006364Tupaia matrix metalloproteinase-27112180
belan eri
1152gi3511149Gallus matrix metalloproteinase663 57
gallus
1153gi11066090Homo Sapiensmatrix metalloprotease 138296
MMP-27
1153gi12006364Tupaia matrixmetalloproteinase-27112180
belan eri
1153gi3511149Gallus matrix metalloproteinase663 57
gallus
1154gi6689894Homo SapiensSuppressor of Fused 2599100
1154gi5739507Homo Sapienssuppressor of fused 259499
1154gi4468628Mus musculusSu(fu) protein 254197
1155gi21667212Homo Sapiensbactericidal/permeability-increasing2600100
protein-like 2
1155gi20387085OncorhynchusLBP (LPS binding protein)/BPI690 31
mykiss (bactericidal/permeability-increasing
protein)-1
1155gi20387087OncorhynchusLBP (LPS binding protein)/BPI685 30
mykiss (bactericidal/permeability-increasing
protein) like-2
1156gi11229139Homo SapiensbB152O15.3 (SRY (sex 2066100
determining
region Y)-box 18)
1156gi12082687Hoano SapiensSry-related HMG-box protein2066100
1156gi8894593Homo SapiensSOX18 protein 2066100
1157gi19526647Homo Sapiensoxidored-vitro domain-containin837 85
protein
1157gi7303522DrosophilaCG13178-PA 172 31
melanogaster
1157gi16304~788Mus musculusbendless-like ubiquitin 83 28
conjugating
enzyme
1158gi19526647Homo Sapiensoxidored-vitro domain-containing837 85
protein
1158gi7303522DrosophilaCG13178-PA 172 31
melanogaster
1158gi16304788Mus musculusbendless-like ubiquitin 83 28
conjugating
enzyme
1159gi1794221Mus musculusDNA ligase III-beta 298789
1159gi1794223Mus musculusDNA ligase III-alpha 298789
1159gi19550955Homo Sapiensligase III, DNA, ATP-dependent2875100
1160gi15667919Homo SapiensSERPINB12 167899
1160gi12597188Homo Sapienssquamous cell carcinoma 749 48
antigen 2
1160gi1235617Homo Sapienssquamous cell carcinoma 749 48
antigen
1161gi15141587Eulemur olfactory receptor 67 34
rubriventer
1161gi21739229Oryza sativaOSJNBa0072F16.8 67 43
1161gi21629328LeishmaniaL3561.8 65 37
maj or
1162gi2589190Homo Sapiensskin-specific protein 68 39
1162gi38232 Pan troglodytesimmunoglobulin alpha 61 39
heavy chain
1162gi14021730Mesorhizobiumc-type cytochrome biogenesis68 31
loti protein
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1163gi7228149Mus musculusATFa-associatedfactor 354 50
1163gi7303705DrosophilaCG12340-PA 193 24
melanogaster
1163gi5052666DrosophilaBcDNA.LD26050 193 24
melanogaster
1164gi20901968CaenorhabditisC. elegans RPL-36 protein71 34
elegans (correspondin sequence
F37C12.4)
1165gi5911451Drosophilacytochrome oxidase III 43 41
nannoptera
1165gi13276253Homo SapiensT-cell receptor beta 56 34
chain VJ region
1165gi3928896Homo SapiensSH2 domain protein lA 55 38
isoform C
1166gi20381326Homo SapiensSimilar to caspase 8, 263 100
apoptosis-related
cysteine protease
1166gi14211398Homo Sapienscaspase-8L 263 100
1166gi19401524Homo Sapiensprocaspase-8 223 95
1167gi10440448Homo SapiensFLJ00060 protein 1204 98
1167gi3983420Homo SapiensKIR3DL1-like natural 693 47
killer cell receptor
1167gi13560453Homo Sapienskiller cell immunoglobulin-like693 47
receptor
3DL1
1168gi1799570Rattus TIP120 4573 99
norvegicus
1168gi7688703Homo sapiensTIP120 protein 4573 99
1168gi5811583Rattus TIP120-family protein 2735 57
TIP120B
norve 'cus
1169' 13016701Homo Sapiensactivating coreceptor 1226 100
NI~p80
1169gi7188567Homo Sapienslectin-like receptor 1226 100
Fl
1169gi22449867Macaca NKp80 NK receptor 1122 90
fascicularis
1170gi14027275Mesorhizobiumnodulation protein node,70 27
3-oxoacyl-(acyl
loti carrier protein) reductase
1170gi1531618Rhizobium NodG 68 26
sp.
N33
1170gi6899062Llreaplasmascryl-tRNA synthctasc 70 31
urealyticum
1171gi3021409Homo Sapienstransducin (beta) like 3057 100
1 protein
1171gi13161069Homo Sapienstransducin beta-like 2548 91
1
1171gi12642596Homo Sapiensnuclear receptor co-repressor/HDAC32431 86
complex subunit TBLRl
1172gi13623421Homo SapiensSimilar to RIKEN cDNA 380 69
5730589L02
gene, clone MGC:13124
IMAGE:4110925, mRNA,
complete cds.
1172gi12803383Homo Sapiensclone MGC:2099 IMAGE:3051525,376 68
mRNA, complete cds.
1172gi13111983Homo Sapiensclone MGC:4221 IMAGE:2958347,376 68
mRNA, complete cds.
1173gi13623421Homo SapiensSimilar to RII~EN cDNA 380 69
5730589L02
gene, clone MGC:13124
IMAGE:4110925, mRNA,
complete cds.
1173gi12803383Homo Sapiensclone MGC:2099IMAGE:3051525,376 68
mRNA, complete cds.
1173gi13111983Homo sapiensclone MGC:4221 IMAGE:2958347,376 68
mRNA, complete cds.
1174gi13623421Homo sapiensSimilar to RII~EN cDNA 1830 99
5730589L02
gene
1174gi19484086Mus musculusRIKEN cDNA 5730589L02 1802 95
gene
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TART,Ti.7 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1174gi1699265Homo Sapiensmalignant cell expression-enhanced930 81
gene/tumor progression-enhanced
gene
1175' 13182755Homo SapiensHPHRP 1210100
1175gi15929309Homo Sapiensphosphotriesterase related1210100
1175gi881499 Mus musculusparathion hydrolase (phosphotriesterase)-106986
related protein
1176gi552075 Chironomusgiant secretory protein 71 28
tentans
1176gi15419013Toxoplasmasubtilisin-like protein 71 34
gondii
1176gi156534 Chironomusgiant secretory protein 66 28
(gsp)
tentans
1177gi5458910PyrococcusFLAGELLA-RELATED PROTEIN103 24
C
abyssi
1177gi487272 EnterococcusNa+ -ATPase subunit F 90 31
hirae
1177gi9229886Ciona ezrin/radixin/moesin 111 27
(ERM)-like protein
intestinalis
1178gi21554060Arabidopsisphytocyanin 44 43
thaliana
1178gi205640 Rattus acetylcholine receptor 53 44
alpha subunit
norvegicus
1178gi4028904Rattus nicotinic acetylcholine 53 44
receptor alpha 4
norvegicussubunit
1179gi 18375961Neurosporarelated to ARCH protein 53 44
crassa
1179gi2935025Rhodococcusprotocatechuate dioxygenase38 38
alpha
opacus subunit
1179gi13421646CaulobacterspoU rRNA methylase family39 40
protein
crescentus
CB 15
1180gi14348558Homo SapienscDNA encoding protease 82 38
domain of
endotheliase 1
1180gi1245184.Danio rerio~g01 66 33
1180gi6137097Homo Sapiensscrine protease DESC1 82 38
1181gi19528151DrosophilaAT26759p 59 35
melanogaster
1181gi16768554DrosophilaGM08606p 59 35
melanogaster
1181gi7291750DrosophilaCG4065-PA 59 35
melano
aster
1182gi13377880Cricetulusarginine N-methyltransferase325385
p82 isoform
longicaudatus
1182gi13377882Cricetulusarginine N-methyltransferase325385
p77 isoform
longicaudatus
1182gi21626587DrosophilaCG9882-PA 121336
melanogaster
1183gi191185 Cricetulusphosphatidylserine decarboxylase113088
griseus
1183gi5921491Homo SapiensdJ858B16.2 (phosphatidylserine122096
decarboxylase (PSSC,
EC 4.1.1.65))
1183gi16306618Homo Sapiensphosphatidylserine decarboxylase122096
1184gi11907580Mus musculusTSC22-related inducible 894 87
leucine zipper
3c
1184gi5231131Homo SapiensTSC-22 related protein 460 98
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1~0
TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1184gi5919161Homo SapiensTSC-22-like Protein 460 98
1185gi13874437Homo Sapienscerebral protein-11 1461 68
1185gi15292367DrosophilaLD47668p 510 41
melanogaster
1185gi2443444Homo SapiensTEX28 310 40
1186gi13543940Homo SapiensSimilar to RIKEN cDNA 2568 99
2610017609
gene
1186gi18204520Mus musculusRIICEN cDNA 2610017609 2381 91
gene
1186gi16923351Homo SapiensRbBP-35 1434 99
1187gi18676660Homo SapiensFLJ00229 protein 931 91
1187gi5824711Caenorhabditissimilar to 7TM chemoreceptor80 20
elegans (srd-
family)
1187gi8825622Rattus T cell receptor 68 36
norvegicus
1188gi17865311Homo Sapiensdipeptidyl peptidase-like4646 100
protein 9
1188gi11095188Homo Sapiensdipeptidyl peptidase 2876 60
8
1188gi21265133Homo SapiensSimilar to dipeptidylpeptidase2217 58
8
1189gi17865311Homo sapiensdipeptidyl peptidase-like4069 100
protein 9
1189gi11095188Homo Sapiensdipeptidyl peptidase 2454 59
8
1189gi21265133Homo SapiensSimilar to dipeptidylpeptidase2455 56
8
1190gi17865311Homo Sapiensdipeptidyl peptidase-like4542 98
protein 9
1190gi11095188Homo Sapiensdipeptidyl peptidase 2810 60
8
1190gi21265133Homo SapiensSimilar to dipeptidylpeptidase2151 57
8
1191gi337508 Homo sapiensribosomal protein 554 99
1191gi57724 Rattus ribosomal protein S25 554 99
rattus
1191gi12805251Mus musculusribosomal protein S25 554 99
1192gi208176 synthetic D2-T antigen 61 40
construct
1193gi7328583Drosophilamechanosensorytransduction851 28
melanogasterchannel
NOMPC
1193gi7385113Bos taurusankyrin 1 777 30
1193gi11065673CaenorhabditisI'71A12B.4 778 28
ele ans
1194gi7672669Homo sapiensserine protease Htra2 1890 100
1194gi12652695Homo sapiensHtrA-like serine protease1890 100
1194gi5870865Homo Sapiensserine protease 1890 100
11951349449 Homo SapiensA3 adenosine receptor 904 100
1195113559064Homo SapiensbA552M11.6 (adenosine 904 100
A3 receptor)
1195120988265Homo Sapiensadenosine A3 receptor 904 100
1196gi21645219DrosophilaCCa15671-PA 299 37
melanogaster
1196gi9864185DrosophilaCrossveinless 2 299 37
melanogaster
1196gi7768636Xenopus I~ielin 276 34
laevis
1197gi18480772Mus musculusolfactory receptor MOR101-21415 84
1197gi18479346Mus musculusolfactory receptor MOR101-11334 82
1197gi3769616Rattus olfactory receptor 973 86
norvegicus
1198gi498768 Serratia Deoxyadenosyl-methyltransferase339 51
marcescens
1198gi10799034Vibrio DNA adenine methylase 332 54
cholerae
1198gi10799036Yersinia DNA adenine methylase 331 52
pseudotubercul
osis
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TART.F ?. A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1199 gi16974751Gallus CALII 338 37
gallus
1199 gi666121Xenopus cpl-1 293 33
laevis
1199 gi1213589Xenopus Prostaglandin D Synthase292 33
laevis
1200 gi22296200Thermosynechoasparaginyl-tRNA synthetase105746
coccus
elongatus
BP-1
1200 gi17132791Nostoc asparaginyl-tRNA synthetase102746
sp. PCC
7120
1200 gi19713460FusobacteriumAsparaginyl-tItNA synthetase101343
nucleatum
subsp.
nucleatum
ATCC 25586
1201 gi18088970Homo SapiensSimilar to RIICEN cDNA 126399
4933400E14
gene
1201 gi20067381Homo SapiensALMS1 protein 249 41
1201 gi21552774Mus musculusAlmstrom syndrome 1 protein219 38
1202 gi347134Homo Sapienssuccinate dehydrogenase 495 92
flavoprotein
subunit
1202 gi12655061Homo Sapienssuccinate dehydrogenase 495 92
complex,
subunit A, flavoprotein
(F )
1202 gi506338Homo Sapiensflavoprotein subunit 495 92
of complex II
1203 gi18490322Homo SapiensSimilar to RII~EN cDNA 224199
6330404M18
enc
1203 gi21928186Mus musculusGPI-gamma 4; GPI amma4 147161
1203 gi17946082DrosophilaI2E54096p 688 47
melanogaster
1204 gi9957165Homo SapiensalphaCP-3 1722100
1204 gi9957161Mus musculusalphaCP-3 170899
1204 gi15082311Homo SapiensSimilar to poly(rC)-binding840 99
protein 3
1205 gi14574118CaenorhabditisC. elegans DPY-19 protein239 31
elegans (corresponding sequence
F22B7.10)
1205 gi12328595HeterodoxusNADH dehg~diogenaSe subuuit7~ 29
2
macropus
1205 gi18378695Bufo maculatesNADH dehydro enase subunit75 24
2
1206 gi189760Homo Sapienspyruvate dehydrogenase 171096
beta-subunit
1206 gi189762Homo Sapienspyruvate dehydrogenase 171096
E1-beta subunit
1206 gi190792Homo Sapienspyruvate dehydrogenase 171096
E1-beta subunit
precursor
1207 gi688292Homo Sapienscalmitine; calsequestrine2029100
1207 gi2618621Mus musculusskeletal muscle calsequestrin193894
1207 gi164842Oryctolaguscalsequestrin 190894
cuniculus
1208 gi22295775Thermosynechoperiplasmic sugar-binding65 35
protein of
coccus sugar ABC transporter
elongates
BP-1
1208 gi2622963Methanothermoconserved protein 59 30
batter
thermautotrophi
cus str.
Delta
H
1208 gi18377999Drysdalia NADH dehydrogenase subunit61 34
1
coronata
1209 gi11034760Homo SapiensNIBAN 369299
1209 gi10432376Homo SapiensbG56G5.1 (novel protein)333499
1209 gi11022733Mus musculusNiban 232067
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~reur ~ ~ w
SEQ Hit ID Species ~ Description S Percentage
ID
scoreidenti
1210 gi2982508Homo SapiensTCR beta chain 129293
1210 gi3002925Homo SapiensT cell receptor beta 128193
chain
1210 gi36733 Homo SapiensT cell antigen receptor 102875
beta chain
1211 gi12006041Homo SapiensAD038 761 98
1211 gi14189960Homo SapiensPR00764 141 53
1211 gi 19072857Homo Sapienslung squamous cell cancer129 60
related protein
LSCC-3
1213 gi2995719Homo Sapiensprotocadherin 43 4792100
1213 gi20072790Homo Sapiensprotocadherin gamma subfamily477799
C, 3
1213 gi5456977Homo Sapiensprotocadherin gamma C3 477799
1214 gi337487Homo SapiensRo ribonucleoprotein 174799
autoantigen (Ro/SS-
A) precursor
1214 gi179882Homo Sapienscalreticulin 174799
1214 gi22203354Cricetuluscalreticulin 168795
griseus
1215 gi200964Mus musculusserene 2 ultra high sulfur319 52
protein
1215 gi3228237Homo sapiensultra high sulfer keratin281 49
1215 gi200962Mus musculusserene 1 ultra high sulfur281 50
protein
1216 gi13940422Macaca ATPase subunit 8 56 31
sylvanus
1217 gi5917716Gallus sprouty 2 60 45
gallus
1217 gi 14275701Influenza matrix protein 2 62 32
virus
1217 gi2738577Homo Sapiensconnexin46.6 54 50
1218 gi17223709Homo Sapiensselenoprotein SeIM 235 100
1218 gi17223711Mus musculusselenoprotein SeIM 188 78
1218 gi7380925Bos taurusFc gamma receptor III 73 45
1219 gi15025778ClostridiumPredicted membrane protein50 36
acetobutylicum
1219 gi13752743Serratia TrpG 65 51
marcescens
1219 gi20906991MethanosarcinaCation transporter 62 29
mazei Goel
1220 gi535358Ncisseria Opa15063G 60 50
gonorrhoeac
1220 gi1480793Neisseria OpaIl 58 47
meningitides
1221 gi992950Homo SapiensOPN-c 142698
1221 gi189151Homo Sapiensnephropontin precursor 137790
1221 gi1001963Homo Sapiensosteopontin 137790
'
1223 gi18088363Homo Sapiensadvanced glycosylation 200499
end product-
specific receptor
1223 gi1841550Homo Sapiensreceptor for advanced 200499
glycosylation end
products
1223 '6691626Homo Sapiensadvanced glycation endproducts200499
receptor
1224 gi3157464Thermus rote al membrane protein77 38
sp. A4~
1224 gi8778370ArabidopsisF15O4.23 65 37
thaliana
1224 gi15156782AgrobacteriumAGR C 3106p 59 34
tumefaciens
str.
C58 (Cereon)
1225 gi37231 Homo SapiensDNA topoisomerase II 806199
,
1225 gi3869382Homo SapiensDNA topoisomerase II 804899
beta
1225 gi790988CricetulusDNA topoisomerase (ATP-hydrolysing)789297
l ongicaudatus
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1226gi10041309Homo sapienshFATPl 3336 98
1226gi1881713Rattus fatty acid transport 3031 87
protein
norvegicus
1226gi10041307Rattus rFATP 3031 87
sp.
1227gi3309176Mus musculusCOP9 complex subunit 796 94
7b
1227gi15215085Mus musculusSimilar to COP9 (constitutive793 93
photomorphogenic), subunit
7b
(Arabidopsis)
1227gi19909525Homo sapiensDERP10 (dermal papilla 467 56
derived protein
10)
1228gi6942096Mus musculusCBLN3 938 93
1228gi180251 Homo Sapiensprecerebellin 551 58
1228gi5702371Mus musculusprecerebellin-1 544 57
1229gi17861952DrosophilaLD01947p 1384 50
melanogaster
1229gi6850946Homo SapiensdJ322I12.1 (novel protein336 100
similar to C.
elegans C05C8.6 (Tr:016313))
1229gi21411108Mus musculusSimilar to BTB domain 211 32
protein BDPL
1230gi8132557Drosophilaankyrin 2 729 30
melano
aster
1230gi710551 Mus musculusankyrin 3 734 29
1230gi1841966Rattus ankyrin 700 30
norvegicus
1231gi21667212Homo Sapiensbactericidal/permeability-increasing2384 98
protein-like 2
1231gi20387085OncorhynchusLBP (LPS binding protein)/BPI672 31
mykiss (bactericidal/permeability-increasing
protein)-1
1231gi20387087OncorhynchusLBP (LPS binding protein)/BPI667 30
myleiss (bactericidal/permeability-increasing
protein) like-2
1232gi21667212Homo Sapiensbactericidal/permeability-increasing2389 99
protein-like 2
1232gi20387085OncorhynchusLBP (LPS binding protein)/BPI664= 31
mykiss (bactericidal/permeability-increasing
protein)-1
1232gi20387087OncorhynchusLBP (LPS binding protein)IBPI659 30
mykiss (bactericidal/permeability-increasing
protein) like-2
1233gi21667212Homo Sapiensbactericidal/permeability-increasing2595 99
protein-like 2
1233gi20387085OncorhynchusLBP (LPS binding protein)/BPI698 31
myleiss (bactericidal/permeability-increasing
protein)-1
1233gi20387087OncorhynchusLBP (LPS binding protein)/BPI693 30
mykiss (bactericidal/permeability-increasing
protein) like-2
1234gi19569876DictyosteliumSIMILAR TO HYPOTHETICAL247 26
26.2
discoideumKD PROTEIN
1234gi2191168Arabidopsiscontains similarity 187 27
to myosin heavy chain
thaliana
1234gi603379 SaccharomycesYer139cp 145 28
cerevisiae
1235gi11493528Homo SapiensPR01953 671 100
1235gi19912632Eulemur HC class II antigen ~ ~ 33
~ 56
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
rubriventer
1235gi19912630Eulemur MHC class II antigen 55 33
macaco
macaco
1236gi17065951Ostertagiacollagen 70 35
ostertagi
1236gi158077 Drosophilaperiod protein 69 38
robusta
1236gi497417 Glycine dehydrin-like protein 81 27
max
1237gi3068592Mus musculuspunc 2396 94
1237gi19570398Homo SapienshDDM36 890 41
1237gi11862941Mus musculusDDM36E 892 41
1238gi12667401Homo SapiensNUF2R 2347 99
1238gi14317902Homo Sapiensleinetochore protein 2347 99
Nuf2
1238gi12667403Mus musculusNUF2R 1754 73
1239gi2494126ArabidopsisContains similarity 94 23
thaliana to Chlamydia outer
membrane protein (gb~X53512).
1239gi19887475MethanopyrusUncharacterized protein68 34
kandleri conserved in
AV 19 archaea
1239gi21646173Chlorobiumribosomal protein S20 67 29
tepidum
TLS
1240121634825Homo Sapienssemaphorin 6D isoform 5658 98
4
1240gi21634823Homo Sapienssemaphorin 6D isoform 3106 96
3
1240gi21634827Homo Sapienssemaphorin 6D isoform 3106 99
1
1241gi9949555Pseudomonasprobable pyruvate dehydrogenase71 35
aeruginosaE1
component, alpha subunit
1241gi48708 MycobacteriumORFal (AA 1 - 74) 58 37
tuberculosis
1241gi307352 Homo Sapiensprothymosin alpha 54 35
1242gi9106331Xylella 3-dehydroquinate synthase43 34~
fastidiosa
9a5c
1242gi13700302Staphylococcusxanthine phosphoribosyltransferase45 35
aureus
subsp.
aureus
N315
1242gi21203529Staphylococcusxanthine phosphoribosyltransferase45 35
aureus
subsp.
aureus
MW2
1243gi21671105Homo SapiensRAD52B 1134 100
1243gi20070921Mus musculusRII~EN cDNA 2410008M22 829 74
gene
1243gi21594785Homo SapiensSimilar to RII~EN cDNA 572 97
2410008M22
ene
1244gi6013381Rattus TM6P1 147 47
norvegicus
1244119353944Mus musculusRIICEN cDNA 2610318618 127 31
gene
1244gi20270909OncorhynchusVHSV-induced protein-6 118 31
mykiss
1245gi6013381Rattus TM6P1 272 36
norvegicus
1245gi21428644DrosophilaLP10820p 256 42
melanogaster
1245gi20270909OncorhynchusVHSV-induced protein-6 190 29
mykiss
1246111993700Homo Sapiensmelastatin 2 1194 100
1246gi3243075Homo Sapiensmelastatin 1 1057 83
1246gi3047242Mus musculusmelastatin 1050 83
1247118044366Homo SapiensSimilar to MEGF10 protein3468 99
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1247gi17386053Mus musculusJedi protein 2280 51
1247gi18252658Mus musculusJedi-736 protein 2280 51
1248gi20987880Mus musculusSimilar to PTH-responsive3586 87
osteosarcoma
B 1 protein
1248'4588087 Homo SapiensPTH-responsive osteosarcoma2264 92
B1 protein
1248gi21595711Homo SapiensSimilar to PTH-responsive1546 100
osteosarcoma
B 1 protein
1249gi19913471Homo sapienssimilar to dJ84N20.1.1 1265 99
(novel protein,
isoform 1)
1249gi13591434Homo SapiensdJ84N20.1.2 (novel protein,1160 100
isoform 2)
1249gi13591435Homo SapiensdJ84N20.1.1 (novel protein,976 99
isoform 1)
1250gi16605581Homo SapiensH-rev107-like protein 1451 100
5
1250'21707989Homo SapiensSimilar to H-rev107-like1376 96
protein 5
125016048565 Homo sapiensretinoid inducible gene382 54
1
1251gi21263094Rattus tramdorin 1 1667 81
norvegicus
1251gi21263092Mus musculustramdorin 1 1664 82
1251gi21908026Mus musculusproton/amino acid transporter1664 82
2
1252gi14571904Rattus lysosomal amino acid 1690 87
norvegicustransporter 1
1252gi21908024Mus musculusproton/amino acid transporter1685 87
1
1252gi21263092Mus musculustramdorin 1 1294 66
1253'21595630Homo SapiensSimilar to forkhead 75 44
box L2
1253gi10580569Halobacteriumtraps lesion repair; 69 51
sp. NRC-1 YqjH
1253gi557673 Sus scrofaBM88 antigen 72 41
1254gi1669500Mus musculusfibroblast growth factor917 90
homologous
factor 1
1254gi1563885Homo Sapiensfibroblast growth factor917 90
homologous
factor 1
1254gi14317951Rattus fibroblast growth factor916 98
norvegicushomologous
factor 1B
1255gi13529143Homo SapiensSimilar to RII~EN cDNA 779 100
1700010H15
ge112
1255gi19263005~ Ciona leucine-rich repeat 759 75
intestinalisdynein light chain
1255gi2760161Anthocidarisouter arm dynein light 656 68
crassispinachain 2
1256gi12666529Mus musculusb,b-carotene-9',10'-dioxygenase2356 80
1256gi4001821Ambystoma RPE65 protein; retinal 1125 44
tigrinum pigment
epithelium 65-protein
1256111990268Mus musculusbeta,beta-carotene 15,15'-dioxygenase1110 42
1257112666529Mus musculusb,b-carotene-9',10'-dioxygenase2305 81
1257_ Ambystoma RPE65 protein; retinal 1122 44
gi4001821ti ~inum pigment
epithelium 65-protein
1257gi11990268Mus musculusbeta,beta-carotene 15,15'-dioxygenase1113 42
1258gi18490501Mus musculusRIKEN cDNA 2010002A20 868 76
gene
1258gi61 Bos tauruscalmodulin-independent 166 29
adenylate ~
cyclase
1258gi15559697Homo SapiensSimilar to neural cell 165 29
adhesion molecule 1
1259gi21748488Homo SapiensFLJ00277 protein 50 52
1259'2331293 Mus musculuspreprocortistatin 73 40
1259gi1335910Rattus preprocortistatin 58 36
norve 'cus
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
126011079734 Mus musculuscitron 1291 94
1260gi3599509Mus musculusrho/rac-interacting 1286 94
citron kinase
1260gi2745840Rattus postsynaptic density 1262 93
norvegicusprotein; citron
1261gi14715029Mus musculusserine (or cysteine) 407 39
proteinase inhibitor,
Glade E (nexin, plasminogen
activator
inhibitor type 1), member
2
1261gi551065 Mus musculusprotease-nexin 1 406 38
1261gi412157 Homo Sapiensglia-derived neurite-promoting397 38
factor
(GdNPF)
1262gi4323581Homo Sapienssenescence-associated 223 97
epithelial
membrane protein
1262gi15214678Homo Sapiensclaudin 1 223 97
1262gi7381083Homo Sapiensclaudin-1 223 97
1263gi21634445Homo SapiensGTP-binding protein 449 57
Sara
1263gi13542685Mus musculusSARI protein 446 54
1263gi8926205Homo SapiensSARI 445 54
1264gi11558264Homo Sapienssphin osine-1-phosphatase697 37
1264gi13447199Homo sapienssphingosine-1-pliosphate683 37
phosphatase
1264gi9623190Mus musculussphingosine-1-phosphate691 38
phosphohydrolase
1265gil4 Bos taurusBoWCl.l 1026 37
1265gi5107945Homo SapiensCD163 1093 40
1265gi312142 Homo SapiensM130 antigen 1093 40
1266gil4 Bos taurusBoWCl.l 1026 37
1266gi5107945Homo SapiensCD163 1093 40
12661312142 Homo SapiensM130 anti en 1093 40
1267gi18873700Necator NADH dehydrogenase subunit69 32
americanus2
1267gi20338417Gallus potassium channel subunit57 31
gallus
1267gi396416 Escherichiasimilar to Neurospora 72 42
coli crassa phosphate-
repressible phosphate
permease
1268gi216194~91Homo Sapienssimilar to expressed 778 100
sequence AW049604
1268gi6572294Homo SapiensbA262A13.1 (novel protein)251 49
1268gi161662 Tribolium zinc finger protein 60 26
castaneum
1269gi21591552Haemophiluscell filamentation-like55 31
influenzaeprotein
biotype
aegyptius
1269gi1762771Pleurodeleshomeodomain-containing 66 35
waltl protein
1269gi19528253DrosophilaGH13327p 53 41
melanogaster
1270118033185Danio rerioUNC45-related protein 3103 73
1270112248757Homo SapiensSMAP-1 2393 57
1270gi12248771Homo sapiensSMAP-lb 2393 57
1271gi21064657DrosophilaRH01479p 185 39
melanogaster
1271gi7304173DrosophilaCG1577-PA 185 39
melanogaster
1271gi20150011PseudomonasMmpIV 89 36
fluorescens
1272gi9366656Trypanosomaprobable similar to 76 55
ring-h2 finger protein
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
brucei rhala.
1272gi6714271ArabidopsisF6N18.7 59 36
thaliana
1272gi10440424Homo SapiensFLJ00047 protein 74 50
1273gi15823642Homo SapiensALS2CR7 2038 100
1273gi2645810Mus musculusPftaire-1 1195 68
1273gi2392814Mus musculusPFTAIRE kinase 1190 67
1274gi2407911Homo Sapiensdifferentially expressed714 96
in Fanconi
anemia
1274gi21595389Homo Sapienssimilar to FYVE finger-containing89 27
phosphoinositide kinase
(1-
phosphatidylinositol-4-phosphate
ldnase)
(PIPSK) (PtdIns(4)P-5-lcinase)
(p235)
1274gi330134 human latency-related protein87 46
1
herpesvirus
1
1275gi21908028Homo Sapiensa disintegrin and metalloprotease4205 97
domain
33
1275gi18147612Homo Sapiensmetalloprotease disintegrin4204 97
1275gi13157560Homo SapiensdJ964F7.1 (novel disintegrin3916 97
and
reprolysin metalloproteinase
family
protein)
1276gi530876 Chlamydomonaamino acid feature: 138 35
Rod protein domain,
s reinhardtiias 266 .. 468; amino
acid feature:
lobular protein domain,
as 32 .. 265
1276gi141852 Actinomycessialidase 137 30
viscosus
1276gi13926258ArabidopsisAT5g10430/F12B17_220 110 34
thaliana
1277gi15291913DrosophilaLD31582p 201 36
melanogaster
1277gi16648042DrosophilaGH07105p 131 39
melanogaster
1277gi164~16111Neurosporarelated to supprcssor 129 43
protein SPT23
crassa
1278gi544755 ~ryctolagusaminopeptidasc N; APN 1016 38
cuniculus
1278gi525287 Susscrofa aminopeptidase N. 1012 39
1278gi205109 Rattus ltidney ~n-peptidase 1004 39
precursor
norve icus
1279gi13559063Homo SapiensbA552M11.5 (novel protein)747 100
1279gi9963863Homo SapiensAD026 738 98
1279gi19263987Homo Sapienssimilar to CMRF35 ANTIGEN131 32
PRECURSOR
1280gi2773306Equus caballustype II colla en 69 31
1280gi3687594Canis familiaristype IIB procollagen 69 31
1280gi8918871YccA of 96 pct identical to 64 26
gp:AB021078 30
plasmi d
ColIb-
P9 [Plasmid
F
1281gi9927307Mus musculusjunctophilin type 3 59 42
1281gi5881591Gallus homeodomain protein 78 38
gallus
1281gi11095167Bacteriophagegp38 76 34
ARl
1282gi13938232Homo SapiensSimilar to RII~EN cDNA 78 32
2610005H11
gene
1282gi13883774MycobacteriumNAD-dependent epimerase/dehydratase83 31
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
tuberculosisfamily protein
CDC 1551
1282gi5881591Gallus homeodomain protein 78 38
gallus
1283gi13938232Homo SapiensSimilar to RIKEN cDNA 78 32
2610005H11
gene
1283gi13883774MycobacteriumNAD-dependent epimerase/dehydratase83 31
tuberculosisfamily protein
CDC1551
12 gi5881591Gallus homeodomain protein 78 38
83 gallus
_ gi15779156Homo SapiensSimilar to RIKEN cDNA 4057 100
1284 1810073N04
gene
1284gi13097045Mus musculusSimilar to RIKEN cDNA 1727 91
1810073N04
gene
1284gi18447388DrosophilaRE05944p 716 32
melanogaster
1285gi21626874DrosophilaCG9410-PB 354 46
melanogaster
1285gi7302281DrosophilaCG9410-PA 354 46
melanogaster
1285gi21166086DictyosteliumNucleoside diphosphate 164 30
discoideumkinase
1286gi20977688Xenopus tumorhead 146 33
laevis
1286gi19070822Mus musculusMyb protein P42P~P 132 29
1286gi9652255~vis ariasDNA binding protein 76 26
pur-alpha
1287gi 1006932Visna virusenvelope polyprotein 61 48
1287gi6469042Mus musculuSC184M protein 73 28
1287gi20988388Mus musculusSimilar to mammary tumor73 28
virus receptor
2
1288gi12309630Homo SapiensbA438B23.1 (neuronal 319 31
leucine-rich
repeat protein)
1288gi6273399Homo Sapiensmelanoma-associated 322 31
antigen MG50
1288gi1504040Homo Sapienssimilar to D.melanogaster322 31
pero~idasin(LJl 1052)
1289gi16769274DrosophilaLD22423p 222 24=
melanogaster
1289gi18700635Homo Sapiensimportin 4 113 23
1289gi13277562Homo SapiensSimilar to RII~EN cDNA 113 23
8430408~15
gene
1290gi21391486Mus musculusleucine-rich repeat 430 43
domain-containing
protein
1290gi21623740Rattus Leucine-rich repeat-containing425 43
norvegicusprotein 3
1290gi21391484Homo Sapiensleucine-rich repeat 392 39
domain-containing
protein
1291gi21624340Homo Sapiensceramide kinase 1611 100
1291gi21624342Mus musculusceramide kinases 1374 86
1291gi16768660DrosophilaHL01538p 292 41
melanogaster
1292gi50369 Mus musculusprecursor protein (AA 204 32
-34 to 244)
1292gi312590 Mus musculusbiliary glycoprotein 204 32
1292gi3549152Homo SapiensR29124_1 187 32
1293gi50369 Mus musculusprecursor protein (AA 204 32
-34 to 244)
1293gi312590 Mus musculusbiliary glycoprotein 204 32
1293gi3549152Homo SapiensR29124_1 187 32
1294121411450Mus musculussimilar to FLJ00179 1159 91
protein
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1294gi18676564Homo sapiensFLJ00179 protein 993 99
1294gi17945392DrosophilaRE17452p 486 59
melanogaster
1295gi7708438Homo SapiensdJ885A10.1 (similar 1020 100
to cerebellin
precursor)
1295gi5702371Mus musculusprecerebellin-1 699 70
1295gi180251 Homo Sapiensprecerebellin 696 74
1296gi3901028Homo Sapiensneurotensin receptor 1436 100
2
1296gi1483580Rattus NTR2 receptor 1073 76
norvegicus
1296gi17646096Mus musculuslow affinity neurotensin1072 77
receptor
1298gi6624583Homo SapiensdJ61B2.1 (bullous pemphigoid1342 100
antigen 1 6
(230/240kD) isoform
3)
1298gi403124 Homo Sapiensbullous pemphigoid antigen9121 92
1298gi15077861Mus musculusbullous pemphigoid antigen6442 67
1-a
1299gi2114176Homo Sapiensp97 homologous protein 100 23
1299gi12654337Homo Sapienscraniofacial development100 23
protein 1
1299gi3341899Homo SapiensBCNT 100 23
1300gi6572294Homo SapiensbA262A13.1 (novel protein)499 100
1300gi21619491Homo Sapienssimilar to expressed 260 42
sequence AW049604
1300gi2460196Monodelphisimmunoglobulin Igh@ 65 37
domestica variable domain
1301gi18676652Homo SapiensFLJ00225 protein 779 100
1301Qi2632952Bacillus yebD 66 51
subtilis
_ gi20749947Drosophilafruitless class I male 50 40
1301 virilis isoform
1302gi18676652Homo SapiensFLJ00225 protein 444 97
1302gi2632952Bacillus yebD 59 48
subtilis
_ gi342299 Macaca preprosomatostatin 226 100
1303 fascicularis
1303gi338288 Homo Sapienspreprosomatostatin I 226 100
1303121619156Homo Sapienssomatostatin 226 100
1304gi1424.9944Hoano sapicnsSimilar to bromodomain-containing109 30
4
1304gi2865615Lcislxmaniaacidic ribosomal protein93 36
peruviana P1
1304gi343452 Tarsius involucrin 114 24
bancanus
1305gi219894 Homo Sapiens80I~-L protein 124 26
1305gi187387 Homo Sapiensmyristoylated alanine-rich122 26
C-kinase
substrate
1305gi13562004Nephila major ampullate spidroin140 33
madagascariens2-like protein
is
1306gi21744725Homo Sapienslycosyl-phosphatidyl-inositol-MAM1548 48
1306gi7529597Homo SapiensdJ402N21.2 (novel protein657 53
with MAM
domain)
1306gi7529598Homo SapiensdJ402N21.3 (novel protein591 52
with
Immunoglobulin domains)
1307gi4455102Brassica pollen-specific protein72 44
rapa BAN102
1307gi4096227OryctolagusIg heavy chain 68 31
cuniculus
1307gi17017359Talaromyces605 ribosomal protein 60 43
emersonii L2
1308gi17429038Ralstonia PROBABLE ACYL-COA 1166 56
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
solanacearumDEHYDROGENASE
OXIDOREDUCTASE PROTEIN
1308gi9948609Pseudomonasprobable acyl-CoA dehydrogenase1121 57
aeruginosa
1308gi13421911Caulobacteracyl-CoA dehydrogenase 1058 54
crescentusfamily protein
CB15
1309gi17429038Ralstonia PROBABLE ACYL-COA 1166 56
solanacearumDEHYDROGENASE
OXIDOREDUCTASE PROTEIN
1309gi9948609Pseudomonasprobable acyl-CoA dehydrogenase1121 57
aeruginosa
1309gi13421911Caulobacteracyl-CoA dehydrogenase 1058 54
crescentusfamily protein
CB 15
1310gi 19070124Mus musculuszinc transporter-like 1087 95
3 protein
1310'20563194Mus musculuszinc transporter 6 1075 94
1310gi9803033CaenorhabditisC. elegans TOC-1 protein279 38
elegans (corresponding
sequence ZC395.3)
1311gi854065 Human U88 260 33
herpesvirus
6
1311gi21928439Homo Sapiensseven transmembrane 174 29
helix receptor
1311gi18893248Pyrococcussmc-like 177 24
furiosus
DSM
3638
1312gi5295832Homo SapiensdJ21018.2 (protein similar1142 100
to collagen)
1312gi6526769Homo SapiensHRIHFB2003 1055 97
1312gi7291408DrosophilaCG11206-PA 738 4~1
melano
aster
1313gi19263985Homo SapiensSimilar to RIKEN cDNA 1565 99
1300017E09
gene
1313gi19528309DrosophilaLD02310p 573 55
melanogaster
1313gi7106870Homo SapiensHSPC24~0 227 30
_ gi22090626Homo SapiensHECT domain protein 1169 99
1314 LASU1 0
1314gi6841194Homo SapiensHSPC272 9665 99
1314gi20151907DrosophilaSD03277p 1833 75
melanogaster
1315gi21542541Homo SapiensSimilar to HTPAP protein766 100
1315gi13182757Homo SapiensHTPAP 473 100
1315gi 14020949Arabidopsisphosphatidic acid phosphatase317 50
thaliana
1316gi21542541Homo sapiensSimilar to HTPAP protein1204 99
1316gi13182757Homo SapiensHTPAP 915 100
1316gi14020949Arabidopsisphosphatidic acid phosphatase460 41
thaliana
1317gi180164 Homo SapiensCD7 antigen protein 1135 93
1317'732757 Homo SapiensCD7 antigen 1135 93
1317gi14424540Homo SapiensCD7 antigen (p41) 1135 93
1319gi16416764Homo SapiensFKSG16 2369 99
1319gi13905212Mus musculusRIKEN cDNA 1200006F02 1833 75
gene
1319gi14715055Homo SapiensSimilar to RIKEN cDNA 418 32
1110002008
ene
1320gi16416764Homo SapiensFKSG16 323 98
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1320gi13905212Mus musculusRII~EN cDNA 1200006F02 257 77
gene
1320gi 14715055Homo SapiensSimilar to RIKEN cDNA 97 33
1110002008
gene
1321gi10834558Rattus proline arginine-rich 392 32
norvegicus end leucine-rich
repeat protein
1321gi21618473Homo Sapiensproline arginine-rich 389 32
end leucine-rich
repeat protein
1321gi1145773Homo sapiensprolar in 389 32
1322gi20258604Homo Sapienssialic acid binding 1473 84
Ig-like lectin 5
1322gi2411475Homo SapiensOB binding protein-2 1473 84
1322gi5759106Homo Sapienssialic acid binding 1473 84
Ig-like lectin-5; siglec-
5
1323gi20258604Homo Sapienssialic acid binding 1375 87
I -like lectin S
1323gi2411475Homo SapiensOB binding protein-2 1375 87
1323gi5759106Homo Sapienssialic acid binding 1375 87
Ig-like lectin-5; siglec-
5
1324gi20987759Homo SapiensSimilar to ADAMTS-like 886 99
1
1324gi15099921Homo SapiensADAM-TS related protein874 98
1
1324gi13183078Homo Sapiensa disintegrin-like and 603 73
metalloprotease
domain with thrombospondin
type I
motifs-like 3
1326gi757915Homo SapiensapoCII protein 427 89
1326gi178836Homo Sapiensapolipoprotein C-II 427 89
1326gi342077Macaca apolipoprotein C-II 371 78
fascicularis
1327gi21619424Homo SapiensSimilar to LOC150580 477 100
1327gi12656449Plasmodium erythrocyte membrane 63 25
falciparum protein 1
1327gi15384029uncultured extracellularprotein 64 31
crenarchaeote
74A4
1329gi16033597Homo SapiensSH2 domain-containing 1003 99
phosphatase
anchor protein 2d
1329gi16033591Homo SapiensSH2 domain-containing 991 99
phosphatase
anchor protein 2b
1329gi1809265~Homo Sapiensimmunoglobulin superfamilyreceptor985 99
translocation associated
protein 3
1330gi4877582Homo Sapienslipoma HMGIC fusion 728 63
partner
1330gi14272235Homo SapiensbA183L8.1 (lipoma HMGIC445 61
fusion
partner)
1330gi15292437Drosophila LP10272p 187 25
melanogaster
1331117426418Mus musculuscalmodulin-related protein788 100
1331gi12060826Homo Sapiensserologically defined 610 77
breast cancer
antigen NY-BR-20
1331gi5932428Myxine calmodulin 316 44
glutinosa
1332gi17862436Drosophila LD27564p 152 26
melano aster
1332gi13311009Homo SapiensNYD-SP16 78 26
1333gi13279251Homo SapiensSimilar to wingless-related2000 100
MMTV
integration site 6
1333gi11693044Homo SapiensWNT6 precursor 2000 100
1333114133265Homo SapiensWNT6 2000 100
1334gi20135611Homo Sapienszinc transporter ZnT-5 463 94
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
1334gi19744304Homo Sapienszinc transporter 5 463 94
1334gi19744306Mus musculuszinc transporter 5 407 85
1335gi18480366Mus musculusolfactory receptor MOR145-1310 74
1335gi21928214Homo Sapiensseven transmembrane 301 77
helix receptor
1335'2447219 Homo sapiensOLF4 295 71
1336120988856Homo Sapiensprotein inhibitor of 3277 100
activated STAT3
1336gi4996563Homo Sapiensprotein inhibitor of 3277 100
activatied STAT3
1336gi17149822Rattus potassium channel regulatory3211 96
norvegicusprotein
KChAP
133714469173 Gallus delta-9 desaturase 1149 71
gallus
1337119908266Chanos stearoyl-CoA desaturase1140 65
chanos
1337gi5738564Ctenopharyngodelta-9-desaturase 1132 70
don idella
1338gi14030861Homo Sapiensparaneoplastic neuronal1830 99
anti en MA1
1338gi18478557Rattus paraneoplastic onconeuronal1752 93
norvegicusprotein MAl
1338gi15929183Homo Sapiensmodulator of apoptosis 990 56
1
1339gi5452942Mus musculusglucosidase II beta-subunit134 56
1339' 163157 Bos taurushigh-mobility-group 120 43
protein
1339gi15076513Mus musculus22 klla neuronal tissue-eniiched131 26
acidic
protein
1341gi11177514Homo Sapienstandem pore domain potassium2234 100
channel
THIN-2
1341gi11177510Rattus tandem pore domain potassium2215 98
norvegicuschannel
THIN-2
1341gi1521S363Homo Sapienspotassium channel, subfamily1346 65
I~, member
13
1342gi14336716Homo Sapienssimilar to FBan0003337 1216 100
1342gi20987336Mus musculusRII~EN cDNA A930016P21 427 50
gene
1342gi19886829MethanopyrusSAM-dependent methyltransferase104 31
kandleri
AVl9
1343gi19570398Homo SapienshI~DM36 1138 43
1343gi11862939Mus muSCUlusI2I~M36 1134=43
1343gi11862941Mus muSCUlusDI~M36E 1125 43
1344gi21744725Homo Sapienslycosyl-phosphatidyl-inositol-MAM4898 98
1344gi7529598Homo sapiensdJ402N21.3 tnovel protein1548 99
with
Immunoglobulin domains)
1344gi7529597Homo sapiensdJ402N21.2 (novel protein1321 94
with MAM
domain)
1345112276198Homo SapiensFI~SG40 1020 100
1345gi12408250Homo SapiensFI~SG28 1020 100
1345'18652934XenopuslaevisMig30 649 49
1346gi16769552I7rosophilaLD38375p 1354 41
melano
aster
1346gi7523707ArabidopsisPutative membrane protein1105 39
thaliana
1346gi1632829PlasmodiumAARP2 protein 467 36
falciparum
1347gi20987450Homo SapiensLOC146433 1162 95
1347gi3093373Mus musculussmall proline-rich protein64 39
2I
1347gi912799 Homo Sapienstype I hair keratin 63 33
1348gi1016012Rattus neural cell adhesion 5093 93
norvegicusprotein BIG-2
precursor
1348gi19913548Homo Sapienssimilar to axonal-associated3630 99
cell adhesion
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID scoreidenti
molecule
1348gi200057 Mus musculusneuronal glycoprotein 3630 64
1349gi15292437DrosophilaLP10272p 441 39
melanogaster
1349'4877582 Homo Sapienslipoma HMGIC fusion 221 28
partner
1349gi16648454DrosophilaSD01285p 162 24
melanogaster
1350gi13097705Homo Sapiensserine (or cysteine) 1925 97
proteinase inhibitor,
Glade A (alpha-1 antiproteinase,
antitrypsin), member
3
1350gi1340142Homo Sapiensalphal-antichymotrypsin1921 97
1350gi4165890Homo Sapiensalpha-1-antichymotrypsin1850 97
precursor
1351gi21618556Homo Sapienstrophinin associated 3134 84
protein (tastin)
1351gi905356 Homo Sapienstastin 3129 84
1351gi7861746Mus musculusGABA-A receptor epsilon-like165 40
subunit
1352gi12053849Homo sapiensDREV protein 1689 100
1352gi12053851Homo SapiensDREVl protein 1676 99
1352112055091Mus musculusDREV protein 1655 97
1353gi14627081Homo Sapienscaspase-1 dominant-negative492 100
inhibitor
Pseudo-ICE
1353gi21707335Homo sapiensSimilar to CARD only 462 100
protein
1353gi186286 Homo Sapiensinterleukin 1-beta convertase445 92
1354gi17431573Ralstonia PUTATIVE LIPGPR~TEIN 82 42
solanacearumTRANSMEMBRANE
1354gi995704 SaccharomycesL3149 69 23
cerevisiae
1354gi1256899SaccharomycesYr1138wp 69 23
cerevisiae
1355gi12034719Mus musculusankyrin-like protein 413 43
1355gi13469729Homo Sapiensbreast cancer anti en 415 49
NY-BR-1
1355gi21618588Homo Sapienstestis-specific ankyrin362 46
motif containing
pl'Otelll
1356gi8272557RattuS protein kinaSe WNI~.1 5439 73
norve icuS
1356gi6933864Homo Sapienskinase deficient protein3408 100
ICDP
1356gi19032238Homo Sapiensprotein Icinase WNI~3 1664 56
1357gi8272557Rattus protein kinase WNICl 5439 73
norvegicus
1357gi6933864Homo Sapienskinase deficient protein1159 98
I~DP
1357gi19032238Homo Sapiensprotein kinase WNK3 530 40
1358gi10946203Homo Sapiensneuromedin U receptor 785 100
2
1358gi9944990Homo Sapiensneuromedin U receptor-type785 100
2
1358gi16877377Homo sapiensneuromedin U receptor 785 100
2
1359gi17861592DrosophilaGH13807p 1234 45
melanogaster
1359gi18376566CaenorhabditisY105E8A.20 964 49
elegans
1359gi9368514Leishmaniamethionyl-tRNA synthetase963 42
maj or
1360gi17389919Homo SapiensSimilar to major histocompatibility819 100
complex, class II, DP
beta 1
1360gi575494 Homo SapiensMHC class II lymphocyte437 72
antigen beta
chain
1360gi188479 Homo SapiensHLA-DPB1 437 72
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TABLE 2 A
SEQ Hit ID Species Description S Percentage
ID . identi
score
1361gi3342737Homo Sapiens826660 2, partial CDS 1025 97
1361gi14625940Homo sapiensinterleukin-10 42 53
1361gi3005997okra yellowAC2 77 35
vein mosaic
virus
1362gi3342737Homo Sapiens826660 2, partial CDS 1001 94
1362gi14625940Homo Sapiensinterleukin-10 42 53
1362gi3005997okra yellowAC2 77 35
vein mosaic
virus
1363gi13991167Homo Sapienssialic acid-binding 2879 99
immunoglobulin-like
lectin-like long splice
variant
1363gi14625822Homo SapiensSiglec-Ll 2879 99
1363gi15824310Pan troglodytessialic acid-binding 2804 97
lectin Siglec-Ll
1364gi20072749Homo Sapienssimilar to interferon 879 100
alpha/beta receptor
1
1364gi571296 Homo SapiensCRFB4 188 27
1364'4028135 Gallus interferon alpha/beta 195 27
anus receptor 1
1365gi8572055Homo Sapiensinterleukin-1 receptor 823 100
antagonist homolog
1
1365gi6049805Homo Sapiensinterleukin-1 receptor 823 100
antagonist homolog
1365'6165334 Homo Sapiensinterleukin-1-like protein-1823 100
1366gi177870 Homo Sapiensalpha-2-macroglobulin 2780 40
precursor
1366gi579594 Homo Sapiensalpha 2-macroglobulin 2775 4~0
690-740
1366gi579592 Homo sapiensalpha 2-macroglobulin 2774 40
690-730
1367gi4574224Fundulus multidrug resistance 287 49
heteroclitustransporter homolog
1367gi19743730Rattus ATP-binding cassette 285 50
norvegicusprotein Blb
1367gi34525 Homo SapiensP-glycoprotein (431 273 50
AA)
13681198922 Mus musculuslymphocyte differentiation713 100
anti en
1368gi198926 Mus musculusLy-6A.2 alloantigen 713 100
1368gi198930 Mus musculusdifferentiation antigen713 100
~ ~ ~ Ly-6E/A
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TABLE 2 B
SEQ Hit Species Description S Percentage_
ID ID I scoredenti
685 gi183150Homo Sapiens chorionic somatomammotropin320 100
CS-5
685 gi23271170Homo Sapiens chorionic somatomammotropin275 96
hormone 2
685 gi28188743Pan troglodytesplacental lactogen 279 98
PL-B
686 gi183178Homo Sapiens hGH-V2 1033 78
686 gi23271170Homo sapiens chorionic somatomammotropin707 92
hormone 2
686 gi28188743Pan troglodytesplacental lactogen 715 94
PL-B
688 gi18088830Homo Sapiens AAH20756 785 100
688 gi183178Homo Sapiens hGH-V2 1051 79
688 gi30582691Homo Sapiens 785 100
689 gi12653501Homo Sapiens SERPINFl protein 2003 95
689 gi30583283Homo Sapiens , member 1 2003 95
689 gi30585311synthetic , member 1 2003 95
construct
690 gi20269957Sus scrofa AF498759_1 phospholipase1033 88
C
delta 4
690 121307610Mus musculus phospholipase C 909 77
delta 4
690 gi571466Rattus norvegicusphospholipase C 893 76
delta-4
691 gi17864023Homo Sapiens AF450090_1 KCCR13L 3524 100
691 gi22760385Homo Sapiens unnamed protein 3515 99
product
691 gi22761016Homo Sapiens unnamed protein 3524 100
product
692 gi12697933Homo Sapiens I~IAA1694 protein 3850 100
692 120380030Mus musculus 4933407C03Rik protein3251 98
692 gi2765254.7Homo Sapiens truncated c-Maf 3506 99
inducing
protein
693 gi437662~ryctolagus interleulcin-8 receptor188 61
cuniculus subtype
B
693 gi511803Homo sapiens interleukin-8 receptor172 57
type B
693 gi576679Homo Sapiens interleukin 8 receptor172 57
B
694 gi32966069Homo Sapiens CD39L2 nucleotidase2514 99
694 gi3335098Homo Sapiens CD39L2 2520 100
694 14691263I-Iomo sapiens 2513 99
695 gi16566319Homo sapiens AF411107_1 G protein-184=399
coupled receptor
695 gi21928620Homo Sapiens seven transmembrane1858 100
helix
receptor
695 gi22293641Homo Sapiens putative orphan 845 51
G protein-
coupled receptor
26
696 '24660226Homo Sapiens C-type lectin-like 14.6090
receptor-1
696 gi7110216Homo sapiens AF200949_1 C-type 1458 90
lectin-like
receptor-1
696 gi7110218Mus musculus AF201457_1 C-type 322 29
lectin-like
receptor 2
698 gi18089247Homo Sapiens AAH20966 Similar 2104 100
to
ectonucleoside triphosphate
diphosphohydrolase
5
698 gi30584801synthetic Homo Sapiens ectonucleoside2104 100
construct triphosphate
diphosphohydrolase
5
698 gi3335102Homo Sapiens CD39L4 2104 100
699 1804761Homo Sapiens putative 247 77
700 gi16184225Drosophila LD24527p 666 42
melanogaster
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TABLE 2 B
SEQ Hit_ID Species Description S Percentage-
ID score
I denti
700 gi27447597Drosophila transcriptional 666 42
adapter 2S
melanogaster
700 gi7298997Drosophila CG9638-PA 666 42
melanogaster
701 gi17225457Homo SapiensAF326917_1 autism-related1272 36
protein 1
701 '27817314Danio rerio 1234 36
701 gi29468246Homo SapiensXTP9 3605 99
702 gi20810589Homo Sapienssimilar to arsenite833 99
inducible
RNA associated protein
702 gi22945274Drosophila CG12795-PA 455 54
melanogaster
702 gi9651711Mus musculusAF224494_1 arsenite687 80
inducible
RNA associated protein
703 gi13241652Rattus norvegicusAF309558_1 supernatant2040 93
protein factor
703 gi13543184Mus musculusSEC14-like 2 2038 93
703 gi6624130Rattus norvegicusAC004832_1 similar 2150 100
to 45 kDa
secretory protein
704 gi11066250Homo SapiensAF197937_1 presenilins1693 86
associated rhomboid-like
protein
704 gi13177766Homo SapiensAAH03653 Similar 1761 99
to
prescnilins associated
rhomboid-like protein
704 gi15559382Homo SapiensAAH14058 presenilins1696 86
associated rhomboid-like
protein
705 gi1864091Rattus norvegicusPSD-95/SAP90-associated4997 95
protein-3
705 gi2454510Homo SapiensPSD-95/SAP90-associated2105 47
protein-2
705 gi6979175Homo SapiensAF119818_1 homolog-2089 47
associated protein
2
706 gi11877274Homo Sapiens 2260 99
706 gi21667210Homo SapiensAF4=65765_1 2260 99
bactericidal/permeability-
increasing protein-like
1
706 gi21706776Homo SapiensBactcricidallpermeability-2253 99
increasing protein-like
1
707 gi16768190Drosophila GH22974p 647 41
melanogaster
707 gi24659527Homo Sapiens 2006 100
707 gi7291716Drosophila CG11388-PA 648 41
melanogaster
708 gi14334082Mus musculusAF367970_1 thymus 479 87
LIM
protein TLP-A
708 gi14335908Mus musculusthymus LIM protein 479 87
TLP-A
708 gi14335909Mus musculusthymus LIM protein 396 90
TLP-B
709 gi12804105Homosapiens AAH02905 Similar 2090 100
to
CG15084 gene product
709 gi13649459Homo SapiensAF250306_1 putative2090 100
SB115
protein
709 gi18204670Mus musculus4930527D15Rik protein1015 96
710 gi1674440Homo Sapienscollagen type IV 4222 51
~ ~ ~ a6 chain
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TABLE 2 B
SEQ Hit Species Description S Percentage_
ID ID score
I denti
710 gi1674441Homo Sapiens collagen type IV 4222 51
a6 chain
710 gi556299IvIus musculusalpha-2 type IV 8126 83
collagen
711 gi438007Gallus gallusalpha-2-macroglobulin1574260
receptor
711 gi7861733Homo Sapiens AF176832_1 low density2365499
lipoprotein receptor
related
protein-deleted
in tumor
711 gi8926243Mus musculus AF270884_1 low density2309892
lipoprotein receptor
related
protein LRP1B/LRP-DIT
712 gi17298315Homo Sapiens candidate tumor 848 100
suppressor
protein
712 gi7861733Homo Sapiens AF176832_1 low density848 100
lipoprotein receptor
related
protein-deleted
in tumor
712 gi8926243Mus musculus AF270884_1 low density731 83
lipoprotein receptor
related
protein LRP1B/LRP-DIT
713 gi13544080Homo Sapiens AAH06171 hypothetical1133 100
protein MGC2731
713 gi20071811Musmusculus 5830411ElORikprotein492 55
713 gi33589496Drosophila LD31278p 4b1 44
melanogaster
714 gi1574.09Drosophila fat protein 3001 40
melano aster
714 gi22945533Drosophila CG17941-PA 2292 34
melanogaster
714 gi7295732Drosophila CG3352-PA 3015 40
melanogaster
715 gi1574.09Drosophila fat protein 3007 40
melanogaster
715 gi22945533Drosophila CG17941-PA 2289 34
melanogaster
715 gi7295732Drosophila CG3352-PA 3021 40
melanogaster
716 gi17865311I-Iomo SapiensAF452102 1 dipeptidyl4370 95
peptidase-like protein
9
716 gi27549552Homo Sapiens dipeptidyl peptidase4370 95
IV-related
protein-2
7_16 gi29293087Homo Sapiens dipeptidyl peptidase4511 95
9
717 gi2689444Homo Sapiens ZNF134 1252 57
717 gi31565347Homo Sapiens LOC284018 protein 1252 57
717 gi9968290Homo Sapiens zinc finger protein1094 47
304
718 gi23468368Mus musculus 1200013F24Rile protein690 90
718 gi27695305Mus musculus 1200013F24Rik protein715 91
718 gi7582294Homo Sapiens AF208853 1 BM-011 881 100
719 gi1620870Ciona intestinalismyo~lasmin-Cl 410 27
719 gi7416982Argopecten myosin heavy chain 255 20
irradians cardiac
muscle s ecific
isoform 1
719 gi7416983Argopecten myosin heavy chain 255 20
irradians cardiac
muscle specific
isoform 2
720 gi13872813Homo Sapiens fibulin-6 13764100
720 gi14575679Homo Sapiens AF156100 1 hemicentin1372099
720 gi3879658Caenorhabditis 1636 29
elegans
721 gi13177673Homo Sapiens AAH03621 1520 45
~
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TABLE 2 B
SEQ Hit ID Species Description S Percentage_
ID score
I dentit
721 gi19354327Homo Sapiens 1520 45
721 gi3822553Gallus gallusnuclear calmodulin-binding2238 61
protein
722 117223626Homo SapiensATP-bindin cassette7963 99
A10
722 gi32350914Homo SapiensATP-binding cassette7943 99
sub-
family A member .
10
722 gi32350969Homo SapiensATP-binding cassette7943 99
sub-
family A member
10
723 gi13374079Homo SapiensTAFII140 protein 3677 99
723 gi13374178Mus musculusTAFII140 protein 3193 84
723 gi28175603Homo SapiensTAF3 protein ' 2772 99
724 gi17429038Ralstonia PROBABLE ACYL-COA 658 61
solanacearumDEHYDROGENASE
OXIDOREDUCTASE
PROTEIN
724 gi22776354Oceanobacillusacyl-CoA dehydrogenase638 63
iheyensis
HTE831
724 gi28280023Mus musculus5730439ElORik protein946 85
725 gi21522768Homo Sapiensunnamed protein 3060 100
product
725 gi24047224Homo SapiensSimilar to EGF-like-domain,3060 100
multiple 6
725 gi6752658Homo SapiensAF186084_1 epidermal3055 99
growth
factor repeat containing
protein
726 gi1453034~2Caenorhabditis 1008 36
elegans
726 gi6531661CaenorhabditisAF195610_1 LIN-41A 1008 36
elegans
726 gi6531663CaenorhabditisAF195611_1 LIN-41B 1008 36
elegans
727 '1504026Homo Sapiens 5833 99
727 gi22725157Homo Sapiensminor histocompatibility5833 99
antigen HA-1
727 gi23272016Homo SapiensSimilar to PTPLl-aSSOCiatcd5690 98
RhoGAP 1
728 gi13274120Homo Sapiens 1467 99
728 '6102996Mus musculus~lanin-3 1018 79
728 gi7160973Homo SapienstTNN3 protein 1213 96
729 gi27463365Homo sapiensa disintegrin-like 8961 99
and
metalloprotease
with
thrombospondin type
1 motifs
9B
729 gi28804249Mus musculusmetalloprotease-disintegrin4974 55
protease
729 gi9581879Homo SapiensAF261918_1 disintegrin5723 99
metalloproteinase
with
thrombospondin repeats
730 gi21063967Drosophila AT05453p 382 31
melanogaster
730 gi5911409Drosophila fuzzy 382 31
melanogaster
730 gi7297412Drosophila CG13396-PA 382 31
melanogaster
731 gi15488017Homo SapiensAF407274_1 EWI2 2302 100
731 gi27497567Homo Sapienskeratinocytes associated2302 100
transmembrane protein
4
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TABLE 2 B
SEQ Hit ID Species Description S Percentage_
ID I scoredenti
731 gi31753233Homo sapiensImmunoglobulin superfamily,2302 100
member 8
732 gi15488017Homo SapiensAF407274_1 EWI2 3200 100
732 gi27497567Homo Sapienskeratinocytes associated3200 100
transmembrane protein
4
732 gi31753233Homo SapiensImmunoglobulin superfamily,3200 100
member 8
733 gi22266726Homo SapiensAF311906_1 LIR-D1 1303 96
precursor
733 gi27497567Homo Sapienskeratinocytes associated1303 96
transmembrane protein
4
733 gi31753233Homo SapiensImmunoglobulin superfamily,1303 96
member 8
734 gi21748480Homo SapiensFLJ00271 protein 605 100
734 gi27497567Homo Sapienskeratinocytes associated513 79
transmembrane protein
4
734 gi31753233Homo SapiensImmunoglobulin superfamily,513 79
member 8
735 gi31455457Homo Sapiensputative NFkB activating583 44
' protein
735 gi7022838Homo Sapiensunnamed protein 1794 99
product
735 gi7293694Drosophila CG7323-PA 339 36
melanogaster
736 gi12804169Homo sapiensAAH0294.2 34.9497
736 gi15779178Homo SapiensAAH14652 Similar 3532 97
to
hypothetical protein
BC002942
736 gi18088939Homo SapiensAAH21143 3494 97
737 gi12836469Mus musculusunnamed protein 3495 87
product
737 gi26351115Mus musculusunnamed protein 3466 87
product
737 gi30721603Mus musculusRAVERl 3466 87
738 gi12002000Homo SapiensAF061732 1 My029 415 100
protein
739 115489209Mus musculusBC013712 protein 266 31
739 121757804=Homo Sapiensunnamed protein 1226 96
product
739 gi26354=220MuS musculusunnamed protein 1130 79
product
740 gi15341806Homo sapienSAAH13073 2008 100
740 gi19528077Drosophila AT24025p 165 38
melanogaster
740 gi21627272Drosophila CG12765-PA 167 24
melanogaster
741 gi23495223Plasmodium AE014834_50 liver 407 23
falciparum stage
3D7 antigen, putative
741 gi32492940Homo Sapiensmedulloblastoma 536 25
antigen MU-
MB-20.201
741 gi9916 Plasmodium liver stage antigen393 24
falciparum
742 gi13161060Homo SapiensAF332217_1 protocadherin3354 58
11
742 gi15054521Homo SapiensAF217288_1 protocadherin-S3362 58
742 -gi9845485Homo SapiensAF169692_1 protocadherin-96235 100
743 ' 16552038Homo Sapiensunnamed protein 2404 99
product
743 121410124Mus musculus3230402E02Rik protein1501 61
743 gi5688958Homo SapiensPMMLP 2405 100
744 gi21734445Rattus norvegicusBMP/Retinoic acid-inducible3987 94
neurai-specific
protein-2
744 gi21734447Rattus norvegicusBMP/Retinoic acid-inducible2948 70
~ ~
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TABLE 2 B
SEQ Hit Species Description S Percentage_
ID ID I scoredenti
neural-specific
protein-3
744 gi30348610Gallus gallusBMP/retinoic acid-inducible2090 52
neural-specific
protein
745 12739353Homo sapiens ZNF91L 2077 69
745 gi27693081Homo Sapiens 2054 71 '
745 gi30421228Homo Sapiens zinc finger protein2486 96
430
746 gi23272677Homo Sapiens Similar to zinc 2472 78
finger protein
208
746 gi26251755Homo Sapiens ZNF431 protein 2480 79
746 gi30421228Homo Sapiens zinc finger protein3174 100
430
747 gi1212965Homo Sapiens transmembrane protein1010 99
747 gi1213221Rattus norvegicustransmembrane protein1006 98
747 gi19683999Homo Sapiens coated vesicle membrane1010 99
protein
748 gi1199524Homo Sapiens acidphosphatase 2147 95
748 gi13111975Homo Sapiens AAH03160 acidphosphatase2143 95
2, lysosomal
748 gi30584617synthetic Homo Sapiens acid 2143 95
construct phosphatase 2, lysosomal
749 gi15625570Homo Sapiens AF411981_1 centaurin3851 95
betas
749 gi28422704Homo Sapiens CENTBS protein 2912 100
_
749 gi30109272Homo Sapiens CENTBS protein 4175 99
750 gi10197642Homo Sapiens AF182421 1 MI~S022 647 100
750 115929423Homo Sapiens Hypothetical protein938 100
FLJ20502
750 gi30277696Mus musculus D5Buc26e protein 423 78
751 gi18614026Homo Sapiens zinc finger DNA 998 4~0
binding
protein p71
751 gi27693858Homo Sapiens zinc fin er protein998 40
398
751 '5630080Homo sapiens AC004890 2 984 36
752 gi11345382Homo Sapiens AF308801_1 vacuolar3724 95
protein
sorting protein
16
752 gi12140290Homo Sapiens 3724 95
752 gi15553046Mus musculuS ~Tpsl6 3628 92
753 gi30141048Homo Sapiens Nogo-66 receptor 2226 100
homolog-1
753 gi30141052Rattus norvegicusNogo-66 receptor 2130 95
homolo -1
753 gi32351287Rattus norvegicusNogo-66 receptor 916 51
homolog 2
754 gi177870Homo Sapiens alpha-2-macroglobulin2718 39
precursor
754 gi25303946Homo Sapiens alpha-2-macroglobulin2718 39
754 gi579592Homo Sapiens alpha 2-macroglobulin2712 39
690-730
755 gi18044501Mus musculus angiopoietin-like 1692 70
3
755 gi4929790Homo Sapiens AF152562_1 angiopoietin-2210 93
related protein
3
755 gi5639997Mus musculus AF162224_1 angiopoietin-1692 70
related protein
3
756 gi200057Mus musculus neuronal lycoprotein4821 87
756 gi29837411Homo Sapiens BIG-2 3898 69
756 gi563133Rattus norvegicusBIG-1 protein 4778 87
757 gi16550078Homo Sapiens unnamed protein 3710 99
product
757 gi28175743Homo Sapiens similar to hypothetical3714 100
protein
FLJ30803
757 gi30354720Mus musculus AI427653 protein 3609 96
7_58 gi26329813Mus musculus unnamed protein 3627 93
product
758 gi28175743Homo Sapiens similar to hypothetical3612 98
protein
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TABLE 2 R
SEQ Hit ID Species ~ Description S scorePercentage_
ID Identi
FLJ30803
758 gi30354720Mus musculus AI427653 protein 3520 95
759 gi21929093Homo Sapiens seven transmembrane1718 88
helix
receptor
759 gi24286029Homo Sapiens G-protein coupled 6772 98
receptor
GPR116
759 gi5525078Rattus norvegicusseven transmembrane5048 72
receptor
760 110440398Homo Sapiens FLJ00032 protein 1257 61
760 111917507Homo Sapiens HPFl protein 1254 62
760 gi15929737Mus musculus similar to KRAB 1249 58
zinc finger
protein KR18
761 gi13097633Homo Sapiens AAH03534 Similar 2325 53
to ATPase,
Class I, type 8B,
member 1
761 gi33440008Homo Sapiens possible aminophospholipid3473 66
translocase ATP8B2
761 gi3628757Homo Sapiens FIC1 2576 53
763 gi11558486Homo Sapiens B-cell lymphoma/leukaemia1314 99
11A short form
763 gi18089267Homo Sapiens AAH21098 1153 100
763 gi30410854Mus musculus 1312 98
764 gi32394378Homo Sapiens forkhead-associated1808 100
domain
histidine-triad
like protein
764 gi32394380Bos taurus forkhead-associated1638 89
domain
histidine-triad
like protein
764 gi32394382Sus scrofa forkhead-associated1681 91
domain
histidine-triad
like protein
765 gi31455403Homo Sapiens aprataxin 241 97
765 gi31455405Homo Sapiens aprataxin 235 100
765 gi32394378Homo Sapiens forkhead-associated241 97
domain
histidine-triad
like protein
766 gi31455403Homo Sapiens aprataxin 318 100
766 gi323943'78Homo Sapiens forkhead-associated318 100
domain
histidine-triad
like protein
766 gi32394382Sus scrofa forkhead-associated307 93
domain
histidine-triad
like protein
767 gi26454883Homo Sapiens hypothetical protein1181 100
HSPC148
767 gi6523797Homo Sapiens AF110775_1 adrenal1181 100
gland
protein AD-002
767 gi6841518Homo Sapiens AF161497_1 HSPC1481178 99
768 gi14009597Homo Sapiens AF282619_1 lysyl 1816 98
oxidase-like
3 protein
768 gi14486600Homo Sapiens AF311313_1 lysyl 1816 98
oxidase-like
3 protein
768 gi15186770Homo Sapiens AF284815_1 lysyl 1816 98
oxidase-like
protein
769 gi22713410Homo Sapiens GYLTL1B protein 3229 100
769 gi3954938Homo Sapiens acetylglucosaminyltransferase-2292 70
like protein
769 gi3954978Mus musculus acetylglucosaminyltransferase-2292 70
like protein
770 gi7209721Mus musculus DD57 2243 88
770 '7209723Homo Sapiens WD-repeat like 2476 99
sequence
770 gi8217485Homo Sapiens 2473 99
771 gi16552001Homo Sapiens unnamed protein 3169 100
product
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TABLE 2 B
SEQ Hit Species Description S Percentage_
ID ID score
Identi
771 ' 18676632Homo Sapiens FLJ00215 protein 1943 99
771 gi21706685Mus musculus 9630058J23Rilc protein860 59
772 gi10799166Homo Sapiens AF305686_1 protein 1915 99
kinase
Njmu-Rl
772 '32425794Homo sapiens NJMU-Rl protein 1888 100
772 gi32450708Homo Sapiens NJMU-Rl protein 1888 100
773 gi13277972Mus musculus phosphatidate 2286 96
cytidylyltransferase
2
773 ' 19344052Homo Sapiens 2376 100
.
773 gi4186023Homo Sapiens CDS2 protein 2376 100
774 gi17511840Homo Sapiens AAH18769 2251 99
774 gi20988879Homo Sapiens Similar to hypothetical2251 99
gene
supported by AL133057;
BC018769; BC009436;
AL133057; AL133057;
AL133057
774 gi29387317Mus musculus 1200011O22Rik protein1792 79
775 gi13936996Human herpesvirusORF73 219 21
8
775 gi2246532Human herpesvirusORF 73, contains 226 19
8 large
complex repeat CR
73
775 gi30526291Saimiriine latency associated 219 31
nuclear
herpesvirus antigen
2
776 gi13477379Homo sapiens TTYH2 protein 1037 41
776 118676664Homo Sapiens FLJ00231 protein 1796 91
776 gi28422735Xenopus laevis 104 40
777 gi16877193Homo Sapiens AAH16860 Gprotein-coupled939 98
receptor, family
C, group 5,
member C
777 gi30583709Homo Sapiens G protein-coupled 939 98
receptor,
family C, group
5, member C
777 gi8118032Homo Sapiens AF207989_1 orphan 939 98
G-protein
coupled receptor
778 115679980Homo Sapiens 0114 protein 930 99
778 gi16769562Drosophila LD38910p 328 47
melanogaster
778 gi7302978Drosophila CG8441-PA 328 47
melanogaster
779 gi10726751Drosophila CG13623-PA 333 53
melano aster
779 gi21430012Drosophila GH27470p 333 53
melanogaster
779 gi7406400Arabidopsis putative protein 317 45
thaliana
780 gi13959018Homo Sapiens AF361746_1 endothelial902 100
cell-
selective adhesion
molecule
780 gi13991773Mus musculus AF361882_l endothelial640 70
cell-
selective adhesion
molecule
780 gi29165726Mus musculus Endothelial cell-selective640 70
adhesion molecule
781 gi15422171Homo Sapiens 22 kDa peroxisomal 1013 100
membrane
protein 2
781 gi297437Rattus norvegicusperoxisomal membrane795 76
protein
781 gi8164184Homo Sapiens 22kDa peroxisomal 1013 100
membrane
protein-like
782 gi7620875StreptococcusAF232324_1 Sic1.19 203 41
pyogenes
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TABLE 2 B
SEQ Hit ID Species Description S Percentage_
ID I scoredenti
782 gi7620883StreptococcusAF232328_1 Sic1.23 203 39
pyogenes
782 gi7621271StreptococcusAF232522_1 Sic1.217203 39
pyogenes
783 gi62877 Gallus gallustype VI collagen 734 42
alpha-2
subunit preprotein
783 gi62881 Gallus gallustype VI collagen 734 42
subunit
alpha2
783 gi62882 Gallus gallustype VI collagen 734 42
subunit
alpha2
784 gi17945608Drosophila RE26969p 829 48
melanogaster
784 gi7292879Drosophila CG1998-PA 829 48
melano aster
784 gi7292910Drosophila CG11162-PA 597 42
melanogaster
785 gi17066106Homo SapiensNovex-3 Titin Isoform8832 99
785 121238650Calotomus titin-like protein 519 62
carolinus
785 gi27696390Xenopus laevisSimilar to titin 816 48
786 gi17979434Arabidopsis putative adenylate 193 22
thaliana kinase
786 gi22136756Arabidopsis putative adenylate 193 22
thaliana kinase
786 gi30180922NitrosomonasAdenylate kinase 201 27
europaea
ATCC
19718
787 gi9967224Macaca fascicularishypothetical protein337 98
788 gi18676610Homo SapiensFLJ00204 protein 195 25
788 '26389725Mus musculusunnamed protein 1390 76
product
788 13002588Mus musculusPlenty of SH3s; 197 24
P~SH
789 gi18676610Homo SapiensFLJ00204 protein 250 26
789 gi26329287Mus musculusunnamed protein 1646 75
product
789 gi26389725Mus musculusunnamed protein 1646 75
product
790 gi12654107Homo SapiensAAI-I00866 531 88
790 ' 13937969Homo sapiensTIMP 1 protein 531 88
790 1189382 Homo Sapienscollagenase inhibitor531 88
791 124660226Homo SapiensC-type lectin-like 1367 90
receptor-1
791 gi7110216Homo SapiensAF200949_1 C-type 1365 90
lectin-like
receptor-1
791 gi7110218Mus musculusAF201457_1 C-type 312 29
lectin-like
receptor 2
792 gi10441350Mus musculusolfactory UDP 1557 68
lucuronosyltransferase
792 gi4753766Homo SapiensUDP glucuronosyltransferase1593 67
792 gi5802604Cavia porcellusUDP glucuronosyltransferase1781 72
UGT2A3
793 gi13325266Homo SapiensAAH04450 hypothetical888 100
protein MGC2650
793 gi3688090Homo SapiensR32611_2 796 91
793 gi6841228Homo SapiensAF161407_1 HSPC289 645 77
794 115488645Mus musculusmethyltransferase 1552 76
Cytl9
794 gi18150409Rattus norvegicusAF393243_1 methyltransferase1518 76
794 gi9963861Homo SapiensAF226730_1 Cytl9 1729 99
795 111877243Homo SapiensSSFl/P2Y11 chimeric3802 95
protein
795 g'i14602631Homo SapiensPeter pan homolog 2080 99
795 gi21619996Homo Sapiens 2080 99
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TABLE 2 B
SEQ Hit_ID Species Description S Percentage_
ID score
I denti
796 gi20330550Homo SapiensAF251706_1 NK inhibitory799 98
receptor precursor
796 gi30962593Homo sapiensAF375481_1 immune 800 99
receptor
expressed on myeloid
cells
splice variant 2
796 gi31790204Homo Sapiensinhibitory receptor805 99
IREMl
797 gi20330550Homo SapiensAF251706_1 NK inhibitory799 98
receptor precursor
797 gi30962593Homo SapiensAF375481_1 immune 800 99
receptor
expressed on myeloid
cells
splice variant 2
797 gi31790204Homo Sapiensinhibitory receptor805 99
IREMl
798 gi20330550Homo SapiensAF251706_1 NK inhibitory1480 94
receptor precursor
798 gi30962591Homo SapiensAF375480_1 immune 1401 93
receptor
expressed on myeloid
cells
splice variant 1
798 131790204Homo Sapiensinhibitory receptor1478 94
IREMl
799 gi18307481Homo Sapiensphosphoinositide-binding2122 100
proteins
799 gi27695704Mus musculusConnector enhancer 678 36
of KSR2
799 gi29691916Rattus norvegicusinteractor protein 1651 _
for cytohesin 79
exchange factors
1
800 gil 1493982Homo SapiensAF208232_1 TLH29 274 72
protein
precursor
800 gi15929988Homo SapiensAAH15423 Similar 424 89
to TLH29
protein precursor
800 gi21618549Homo SapiensTLH29 protein precursor274 72
801 gi11493982Homo SapiensAF208232_1 TLH29 303 70
protein
precursor
801 gi15929988Homo SapiensAAH15423 Similar 445 100
to TLH29
protein precursor
801 gi2161854~9Homo SapiensTLH29 protein precursor303 70
802 gi12082723~'aalluS AF293805_1 B cell 2825 69
gallus
phosphoinositide
3-kinase
adaptor
802 gi12082725Mus musculusAF293806_1 B cell 3557 84
phosphoinositide
3-kinase
adaptor
802 gi12082811Callus gallusAF315784_1 B cell 2330 73
phosphoinositide
3-lcinase
adaptor
803 gi7959809Homo SapiensAF116721_55 PR~1082545 100
804 gi15384841Homo Sapiensactivatin NK receptor1684 99
804 gi15384843Homosapiens NTB-Areceptor 1700 100
804 gi9887089Mus musculusAF248635_1 lymphocyte615 43
anti en 108 isoform
1
805 gi10177621Arabidopsis phytoene dehydrogenase-like195 75
thaliana
805 gi17979255Arabidopsis AT5g49550/K6M13_10 211 72
thaliana
805 gi29028742Arabidopsis At5g49550/K6M13 211 72
thaliana 10
806 ' 14270364Mus musculusEpigen protein 378 71
806 gi6272269Rattus norveNC1 rotein 122 52
'cus
806 gi7799191Mus musculustomore ulin-1 122 52
807 gi14270364Mus musculusEpigen protein 378 71
807 gi6272269Rattus norvegicusNCl protein 122 52
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TABLE 2 R
SEQ Hit ID Species Description S scorePercentage-
ID Identi
807 7799191 Mus musculus tomoregulin-1 122 52
808 gi14270364Mus musculus Epigen protein 378 71
808 gi6272269Rattus norvegicusNC1 protein 122 52
808 gi7799191Mus musculus tomoregulin-1 122 52
809 gi27469556Homo Sapiens Putative neuronal 212 39
cell adhesion
molecule
809 gi29289929Danio rerio neogenin 185 39
809 gi3068592Mus musculus punc 198 41
810 gi30348897Homo Sapiens organic solute 643 99
transporter beta
810 gi30348901Ivlus musculusorganic solute 365 62
transporter beta
811 gi18650584Homo Sapiens retinoic acid early1070 94
transcript 1
811 gi18650588Homo Sapiens retinoic acid early1124 99
transcript 1
811 gi21961213Homo Sapiens UL16 binding protein1070 94
2
812 gi13872813Homo Sapiens fibulin-6 485 30
812 gi14575679Homo Sapiens AF156100_1 hemicentin485 30
812 '9280405Homo Sapiens AF245505_1 adlican1372 46
813 gi13872813Homo Sapiens fibulin-6 861 29
813 gi14575679Homo Sapiens AF156100_1 hemicentin857 29
813 gi9280405Homo Sapiens AF245505_1 adlican2436 35
814 gi13872813Homo Sapiens fibulin-6 861 29
814 gi14575679Homo Sapiens AF156100_1 hemicentin857 29
814 gi9280405Homo Sapiens AF245505 1 adlican2436 35
815 gi21619635Homo sapiens similar to Alu 267 60
subfamily S(~
sequence contamination
warning entry
815 gi3002527Homo Sapiens neuronal thread 244 62
protein AD7c-
NTP
815 gi6650810Homo Sapiens AF118094 21 PR~1902261 63
816 gi12240284Mus musculus AF327059_1 apolipoprotein1300 72
AS
816 gi6707433Homo Sapiens AF202889_1 apolipoprotein1864 100
AS
816 gi6707435Homo Sapiens AF202890_1 apolipoprotein1864 100
AS
817 gi12240284Mus musculus AF327059_1 apolipoprotein1300 72
AS
817 gi6707433Homo Sapiens AF202889_1 apolipoprotein1864 100
AS
817 gi6707435Homo Sapiens AF202890_1 apolipoprotein1864 100
AS
818 gi13111784Homo Sapiens AAH03081 hypothetical1720 99
protein FLJ10637
818 gi13543037Mus musculus 4933424BO1Rik protein958 80
818 gi14249965Homo Sapiens AAH08368 hypothetical1724 100
protein FLJ10637
819 gi19344001Homo Sapiens phospholipase A2, 846 99
group IID
819 gi5771420Homo Sapiens AF112982_1 group 852 100
IID
secretory phospholipase
A2
819 gi6453793Homo Sapiens AF188625_1 phospholipase846 99
A2
820 gi21751722Homo sapiens unnamed protein 688 84
product
820 126342939Mus musculus unnamed protein 496 59
product
821 gi11094019Homo Sapiens AF305057 2 RTS 2116 96
beta
821 gi1150421Homo Sapiens rTSbeta 2122 96
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TABLE 2 B
SEQ Hit ID Species ~ Description S_scorePercentage_
ID
Identi
821 gi12654883Homo SapiensAAH01285 rTS beta 2122 96
protein
822 gi12803167Homo SapiensAAH02387 nucleosome1728 99
assembly protein
1-like 1
822 gi189067Homo SapiensNAP 1728 99
822 gi30582885Homo Sapiensnucleosome assembly1728 99
protein
1-like 2
823 gi13432042Homo Sapiensintegrin-linked 2009 99
kinase-
associated serine/threonine
phosphatase 2C
823 gi16306907Homo sapiensAAH06576 integrin-linked2009 99
lcinase-associated
serine/threonine
phosphatase
2C
823 120072498Musmusculus 0710007A14Rikprotein1926 94
824 gi28175169Mus musculus1300015B04Rik protein835 73
824 gi28848867Homo SapiensURGl l 1164 100
824 gi7768636Xenopus laevisI~ielin 239 36
825 gi21928259Homo Sapiensseven transmembrane1023 100
helix
receptor
825 gi21928496Homo Sapiensseven transmembrane1023 100
helix
receptor
825 gi21928655Homo Sapiensseven transmembrane916 89
helix
receptor
826 gi18480746Mus musculusolfactory receptor 1278 79
M~R261-10
826 gi21928655Homo Sapiensseven transmembrane1456 93
helix
receptor
826 gi32052225Mus musculusolfactory receptor 1278 79
GA_x6I~02T2P3E9-4341246-
4340281
827 gi4760780Mus musculusTen-m3 364 95
827 gi5307761Danio rerio ten-m3 310 78
827 gi6760369Mus musculusAF195418_1 ~DZ3 364 95
828 gi16265938Homo SapiensAF314817_1 FI~SG15 2437 98
828 gi21205852Homo SapiensAF3854~29_1 T-cell 3756 100
activation
Rho GTPase activating
protein;
TA-GAP
828 gi21205854Homo SapiensAF385430_1 T-cell 2850 100
activation
Rho GTPase activating
protein
splice variant 1;
TA-GAP
829 gi10432396Homo Sapiens 383 62
829 gi30908443Homo SapiensCUB and sushi multiple388 63
domains 2
829 gi30908445Homo SapiensCUB and sushi multiple549 100
domains 3
830 gi10432396Homo Sapiens 383 62
830 gi30908443Homo SapiensCUB and sushi multiple388 63
domains 2
830 gi30908445Homo SapiensCUB and sushi multiple549 100
domains 3
831 gi3342148Chlamydomonasmyosin heavy chain 499 37
reinhardtii
831 gi532124Dictyosteliummyosin IC 517 41
discoideum
831 gi8953751Arabidopsis myosin heavy chain 492 41
thaliana MYA2
832 gi6472600Chara corallinaunconventional myosin621 38
heavy
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TABLE 2 B
SEQ Hit Species Description S Percentage-
ID ID I scoredenti
chain
832 gi8953751Arabidopsis myosin heavy chain 621 38
thaliana M1'A2
832 gi9453839Chara corallinamyosin 621 38
834 gi21265163Homo Sapiens 2424 99
834 gi7248845Homo sa iens AF231124 1 testican-12428 99
834 gi793845Homo Sapiens testican 2428 99
835 gi20380774Homo Sapiens 2930 99
835 gi22761091Homo Sapiens unnamed protein 2350 99
product
835 gi27502762Mus musculus hypothetical protein2712 90
MGC28931
836 gi20380774Homo Sapiens 2946 100
836 gi22 Homo Sapiens unnamed protein 2366 100
761091 product
836 _ Mus musculus hypothetical protein2728 91
gi27502762 MGC28931
837 gi17391348Homo Sapiens AAH18615 Similar 664 100
to brain
expressed, X-linked
1
837 gi7689029Homo Sapiens AF220189_1 uncharacterized664 100
hypothalamus protein
HBEX2
837 gi9963771Homo Sapiens AF183416_1 ovarian 664 100
granulosa
cell 13.0 kDa protein
h6R74
homolo
838 gi15215122Mus musculus chondroadherin 428 31
838 gi29571143MuS museulus 5430427N1112i1c 430 27
protein
838 gi30908853Homo Sapiens synleurin 3201 100
839 gi12842465Mus musculus unnamed protein 567 92
product
839 gi15488920Homo Sapiens AAH13587 Similar 632 100
to RIKEN
cDNA 2010107623
gene
839 gi19354289Mus musculuS RIICEN cDNA 2010107623567 92
gene
840 ' 16549697Homo Sapiens unnamed protein 2483 99
product
840 gi20988071Mus musculus 2600011E07Rik protein919 80
840 gi21619776Homo Sapiens Similar to I~IICEN 2491 100
cI~NA
2600011E07 ~ene
841 gi12963869Mus musculuS gene trap ankyrin 223 30
repeat
containing protein
841 gi28565117Drosophila myosin phosphatase 228 22
melanogaster DMBS-S
841 gi30138665Nitrosomonas Ankyrin-repeat 228 31
europaea ATCC
19718
842 gi12408272Homo Sapiens apolipoprotein L-IV1742 100
splice
variant a
842 gi12408286Homo Sapiens apolipoprotein L-IV1742 100
splice
variant a
842 gi13374351Homo sapiens AF305226_1 apolipoprotein1725 99
L4
843 gi12408272Homo Sapiens apolipoprotein L-IV1737 99
splice
variant a
843 gi12408286Homo Sapiens apolipoprotein L-IV1737 99
splice
variant a
843 gi13374351Homo Sapiens AF305226_1 apolipoprotein1720 99
L4
844 gi21744725Homo Sapiens AF478693_1 glycosyl-2296 100
phosphatidyl-inositol-MAM
844 gi25005318Sus scrofa MAM domain containing1804 93
~ ~
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TABLE 2 B
SEQ Hit ID Species Description S Percentage_
ID score
I denti
glycosylphosphatidylinositol
anchor 1
844 gi25005320Sus scrofa glycosylphosphatidylinositol1673 92
anchor 1 protein
845 gi21744725Homo SapiensAF478693_1 glycosyl-5051 100
phosphatidyl-inositol-MAM
845 gi25005318Sus scrofa MAM domain containing4481 95
glycosylphosphatidylinositol
anchor 1
845 gi25005320Sus scrofa glycosylphosphatidylinositol4350 95
anchor 1 protein
846 gi1066493SaccharomycesYpr144cp 572 30
cerevisiae
846 gi32487557Oryza sativaOSJNBa0013K16.9 565 32
(japonica
cultivar-
oup)
846 gi4007758SchizosaccharomyceSPBC1604.06c 613 33
spombe
847 gi14280050Homo SapiensVps39/Vam6-like 3913 88
protein
847 gi14701768Homo SapiensVam6Nps39-like protein3990 89
847 gi23273399Homo Sapiens 4079 98
848 gi23273399Homo Sapiens 4095 99
848 gi25059032Mus musculus 3128 72
848 gi29467442Homo Sapienscytosolic phospholipase1512 4~1
A2
delta
849 gi14603301Homo SapiensHypothetical protein986 100
FLJ11749
849 gi7291437Drosophila CG4071-PA 510 49
melanogaster
849 gi9955513Arabidopsis putative protein 340 36
thaliana
850 gi13161409Mus musculusfamily 4 cytochrome444 73
P450
850 gi13182964Mus musculusAF233643_1 cytochrome196 38
P450
CYP4F13
850 gi 13278244Mus musculuscytochromo P450, 196 38
family 4~,
subfamily f, polypeptide
13
851 gi10944887Homo SapiensFGFR-like protein 2475 98
851 gi13183618Homo SapiensAF312678_1 FGF homologous2424 97
factor receptor
851 gi13447749Homo SapiensAF279689_1 fibroblast2475 98
growth
factor receptor
5
852 110944887Homo SapiensFGFR-like protein 2701 99
852 gi13183618Homo SapiensAF312678_1 FGF homologous2650 98
factor receptor
852 gi13447749Homo SapiensAF279689_1 fibroblast2701 99
growth
factor receptor
5
853 110944887Homo SapiensFGFR-like protein 583 98
853 gi13183618Homo sapiensAF312678_1 FGF homologous583 98
factor receptor
853 gi13447749Homo sapiensAF279689_1 fibroblast583 98
growth
factor receptor
5
854 gi12667446Rattus norvegicusAF336854_1 synaptotagmin2034 95
VIIs
854 gi6136786Mus musculussynaptotagmin VII 2025 95
854 gi643656Rattus norvegicussynaptotagmin VII 2034 95
855 gi12053709Homo Sapienswith thrombospondin8842 100
type 1
motif, 12
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TABLE 2 B
SEQ Hit Species Description S Percentage_
ID ID I scoredenti
855 gi27817773Mus musculus metalloprotease 7094 80
disintegrin 12
protein
855 gi5923788Homo Sapiens AF140675_1 zinc 2471 51
metalloprotease
ADAMTS7
856 gi15929988Homo Sapiens AAH15423 Similar 179 48
to TLH29
protein precursor
857 gi13542874Mus musculus Similar to RII~EN 1301 74
cDNA
2210412D01
857 gi17391206Mus musculus RII~EN cDNA 2210412D011591 94
857 gi28277574Danio rerio Similar to RIKEN 1377 79
cDNA
2210412D01 gene
858 gi13542874Mus musculus Similar to RIKEN 1301 72
cDNA
2210412D01
858 gi17391206Mus musculus RIKEN cDNA 2210412D011591 94
858 gi28277574Danio rerio Similar to RIKEN 1343 79
cDNA
2210412D01 gene
859 gi20071312Mus musculus 4933425F03Rik protein1219 80
859 gi217732~ryctolagus macrophagescavengerreceptor602 38
cuniculus type I subunit
859 gi33391740Homo Sapiens MGC45780 1521 98
860 gi20071312Mus musculus 4933425F03Rilc protein1321 86
860 gi33391740Homo Sapiens MGC45780 1656 87
860 gi6478784Mus musculus scavengei receptor 679 34
type A SR-
A
861 gi11493463Homo Sapiens AF130117 38 PR~2852298 75
861 gi21748687Homo Sapiens unnamed protein 319 72
product
861 gi28801453Homo Sapiens unnamed protein 325 77
product
862 ' 14456629Homo Sapiens 1232 50
862 gi15081398Homo Sapiens AF395541_1 kruppel-like~ 54
zinc 1245
finger protein
862 gi29476835Homo Sapiens 1222 47
863 gi16551721Homo Sapiens unnamed protein 3124 99
product
863 gi21320872MuS muSCUlus Cog8 2744 87
863 gi7297851Drosophila CG6488-PA 1143 43
melanogaster
864 gi16307258Homo Sapiens AAH09717 hypothetical942 100
protein
864 gi22945521Drosophila CG31922-PA 165 33
melanogaster
864 gi7242597Homo Sapiens hypothetical protein942 100
865 gi23274241Homo Sapiens KIAA1892-lilee 2039 86
865 gi26332114Mus musculus unnamed protein 1964 82
product
865 gi26345386Mus musculus unnamed protein 1964 82
product
866 gi1562~885Homo Sapiens I'IAA1913 protein 2495 100
866 gi26339494Mus musculus unnamed protein 2312 90
product
866 gi28279830Homo Sapiens KIAA1913 protein 2495 100
867 ' 1000448Rattus norvegicusRat kidney AGT2 2202 81
precursor
867 gi12406973Homo Sapiens alanine-glyoxylate 2740 100
aminotransferase
2
867 gi1944136Rattus norvegicusbeta-alanine-pyruvate2249 83
aminotransferase
868 11000448Rattus norvegicusRat kidney AGT2 1583 84
precursor
868 gi12406973Homo Sapiens alanine-glyoxylate 1870 98
aminotransferase
2
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TABLE 2 B
SEQ Hit_ID Species Description S Percentage_
ID I scoredenti
868 gi1944136Rattus norvegicusbeta-alanine-pyruvate1630 86
aminotransferase
869 gi26892205Homo Sapiens 1 448 39
869 gi29436673Mus musculus 1700049K14Rik protein1732 99
869 gi4165315Sus scrofa kallikrein 452 41
870 gi17985046Brucella melitensisGLYCOSYL TRANSFERASE130 28
16M
870 gi20515259Thermoanaerobacterpredicted glycosyltransferases133 32
tengcongensis
870 gi4455730Streptomyces putative transferase140 32
coelicolor
A3(2)
872 gi13649477Homo Sapiens AF250309_1 putative1998 100
cytokine
receptor CRL4 precusor
872 gi30584223synthetic Homo Sapiens interleukin1998 100
construct 17B
receptor
872 gi8705222Homo Sapiens AF212365_1 IL-17B 1998 100
receptor
873 gi18676472Homo Sapiens FLJ00133 protein 6475 100
873 gi20379832Homo Sapiens FLJ00133 protein 3072 94
873 gi29568116Mus musculus secreted protein 3973 84
SST3
875 gi14249936Homo Sapiens AAH08349 Similar 2581 100
to S-
adenosylhomocysteine
hydrolase-like 1
875 gi16588687Homo Sapiens AF315687_1 S- 2429 92
adenosylhomocysteine
hydrolase-like protein
875 gi27692283Mus musculus S-adenosylhomocysteine2429 92
hydrolase-lilee
1
876 gi14279990Homo Sapiens AF294842_1 ubiquitin458 100
UBF-fl
876 gi29791813Homo Sapiens Ubiquitin-conjugating212 74
enzyme
E2C, isoform 1
876 gi30583439Homo Sapiens ubiquitin-conjugating212 74
enzyme
E2C
877 gi20086516Homo sapions AF245303_1 prominin-24~24~199
variant A
877 gi20086518Homo sapiens AF245304_1 prominin-24241 99
variant B
877 '24637566Rattusnorvegicusprominin-2 3224 74
878 129351676Homo Sapiens An iopoietin-like 2104 100
5
878 129468510Homo Sapiens putative fibrinogen-like2099 99
protein
878 gi29791750Homo sapiens angiopoietin-like 392 37
1
879 gi29351676Homo Sapiens Angiopoietin-like 2100 99
5
879 gi29468510Homo Sapiens putative fibrinogen-like2095 99
protein
879 gi29791750Homo sapiens angiopoietin-like 392 37
1
880 129351676Homo Sapiens Angiopoietin-like 2100 99
5
880 gi29468510Homo Sapiens putative fibrino 2095 99
en-like protein
880 gi29791750Homo Sapiens angiopoietin-like 392 37
1
881 gi11493483Homo Sapiens AF130117 48 PRO2550319 66
881 gi1872200Homo Sapiens alternatively spliced303 56
product
usin exon 13A
881 gi7770139Homo Sapiens AF119917 13 PR01722318 69
882 gi13543706Homo Sapiens AAH06003 349 100
882 gi20988061Mus musculus 1810b13D10Rik protein333 92
882 gi21619079Homo Sapiens 349 100
883 gi11493652Homo Sapiens AF200708 1 calcium 2552 100
~ ~ ~ channel
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TABLE 2 B
SEQ Hit_ID Species Description S Percentage_
ID I scoredenti
Mocker resistance
protein
CCBR1
883 gi13924720Homo sapiensAF252872_1 cystine/glutamate2552 100
transporter xCT
883 gi15082352Homo SapiensAAH12087 member 2552 100
11
884 gi14252988Homo SapiensSRPKlaprotein kinase2297 86
884 gi23468345Homo SapiensSFRS protein kinase2304 87
1
884 gi507213Homo Sapiensserine kinase 2297 86
885 gi18044358Homo SapiensAAH19883 Similar 270 57
to lectin-
like NK cell receptor
885 gi9837288Homo SapiensC-type lectin 270 57
885 gi9837292Homo SapiensC-type lectin 270 57
886 gi22164066Homo SapiensAF388385_1 neurolilastoma-7571 99
amplified protein
886 gi30353863Homo sapiensNAG protein 7227 99
886 gi4337460Homo Sapiensneuroblastoma-amplified6886 99
protein
887 gi22164066Homo SapiensAF388385_1 neuroblastoma-7309 96
amplified protein
887 gi30353863Homo SapiensNAG protein 6965 96
887 gi4337460Homo sapiensneuroblastoma-amplified6624 96
protein
888 gi18645094uncultured M20/M25/M40 family 383 38
proteobaeteriumpeptidase, putative
888 119387947Mus musculusLOC212933 protein 510 73
888 gi28806353Vibrio putative M20/M25/M40387 35
parahaemolyticusfamily
peptidase
889 gi11558029Homo sapiensorganic ration transporter1857 99
889 gi18088251Homo SapiensAAH20565 Similar 1839 95
to hBOIT
for potent brain
type organic
ion transporter
889 '9663117Homo Sapiensorganic ration transporter1849 99
890 gi21732438Homo Sapienshypothetical protein977 100
890 gi26330392MuS muSCUlusunnamed protein 765 80
product
890 gi26390211Mus musculusunnamed protein 765 80
product
891 gi13375149Homo Sapiens 853 90
891 gi20072584Mus musculuscDNA sequence BC027127259 37
891 gi7259265Mus musculusre 'on 277 47
892 gi16589003Homo SapiensAF386649_1 bromodomain-6353 99
containing 4
892 gi18308125Mus musculusAF461395_1 bromodomain-5992 92
containing protein
BRD4 long
variant
892 gi9931486Mus musculusAF273217_1 cell 5994 92
proliferation
related protein
CAP
893 gi15420828Homo SapiensAF397392_1 NOE3-1 2504 99
893 gi19386926Rattus norvegicusAF442822_1 optimedin2484 98
form B
893 gi19386930Mus musculusAF442824 1 optimedin2484 98
form B
894 gi22209078Homo Sapienshypothetical protein4474 99
DKFZp566D234
894 gi26337809Mus musculusunnamed protein 4135 91
product
894 gi6330966Homo SapiensKIAA1263 protein 4492 100
895 gi12654031Homo sapiensAAH00819 Similar 1538 99
to CG6950
gene product
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TABLE 2 B
SEQ Hit ID Species D escription S scorePercentage_
ID
I denti
895 gi5002565Takifugu rubripescysteine conjugate1235 55
beta-lyase
895 gi758591Homo Sapiens glutamine--phenylpyruvate1193 51
aminotransferase
896 '14017833Homo Sapiens KIAA1808 protein 2905 99
896 gi21666433Mus~musculus AF404775_1 actin-binding1498 60
LIM protein 1 medium
isoform
896 gi30259308Mus musculus actin-binding LIM 2799 86
protein 2
897 gi2062399Rattus norvegicusprotein serine/threonine818 52
kinase
CPG16
897 gi6716518Mus musculus AF1551 doublecortin-like818 52
kinase
897 gi6716522Mus musculus AF155821 1 CPG16 818 52
898 gi2062399Rattus norvegicusprotein serine/threonine818 52
kinase
CPG16
898 gi6716518Mus musculus AF1551 doublecortin-like818 52
kinase
898 gi6716522Mus musculus AF155821_1 CPG16 818 52
899 gi13436035Mus musculus prostaglandin E 1583 83
synthase 2
899 gi29179467Danio rerio Similar to prostaglandin1079 60
E
synthase 2
899 gi9280108Macaca fascicularismembrane-associated1907 97
prostaglandin E
synthase-2
900 gi12805247Mus musculus Complement component945 70
1, q
subcomponent, alpha
polypeptide
900 gi20988805Homo Sapiens complement component1308 99
1, q
subcomponent, alpha
polypeptide
900 gi4894854Homo Sapiens AF135157_1 complement1308 99
Clq
A chain precursor
901 gi 12841760Mus musculus unnamed protein 928 80
product
901 gi 12846817Mus musculus unnamed protein 931 80
product
901 gi30802090Homo Sapiens Similar to RIKEI~11127 100
cDNA
1810059622 gene
902 gi21707458Homo Sapiens PAS transcription 2704 87
activation
domain interacting
protein 1
like
902 gi2565046Homo Sapiens CAGF28 3771 97
902 gi4336734Mus musculus Pax transcription 4115 77
activation
domain interacting
protein PTIP
903 114164561Xenopus laevisAF172855 1 Swift 467 79
903 gi4336734Mus musculus Pax transcription 531 93
activation
domain interacting
protein PTIP
904 gi15929776Homo Sapiens AAH15309 growth 135 41
suppressor
1
904 gi23271416Mus musculus Leprel protein 135 41
904 gi30582917Homo Sapiens 1 135 41
905 gi2443352Mus musculus platelet glycoprotein149 45
Ib beta
905 gi30908853Homo sapiens synleurin 1549 100
905 gi6808603Homo Sapiens AF169675_1 leucine-rich147 40
repeat transmembrane
protein
FLRT1
906 gi13991167Homo Sapiens sialic acid-binding1174 100
immunoglobulin-like
lectin-like
long splice variant
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TART.F'7 R
SEQ Hit ID Species Description S scorePercentage_
ID Identi
906 gi14625822Homo Sapiens AF282256 1 Siglec-Ll1174 100
906 gi23272769Homo Sapiens SIGLEC-like 1 1174 100
907 gi13435476Mus musculus DNA segment, Chr 900 95
10,
University of California
at Los
Angeles 1
907 gi28279553Danio rerio Similar to DNA 750 87
segment, Chr
10, University
of California
at
Los Angeles 1
907 gi29144983Mus musculus DNA segment, Chr 657 67
6, ERATO
Doi 253, expressed
908 gi1504040Homo Sapiens 4470 56
908 gi6273399Homo Sapiens AF200348_1 melanoma-4470 56
associated antigen
MG50
908 gi7292259Drosophila CG12002-PA 2536 36
melanogaster
909 gi1504040Homo sapiens 4470 56
909 gi6273399Homo sapiens AF200348_1 melanoma-4470 56
associated antigen
MG50
909 gi7292259Drosophila CG12002-PA 2536 36
melanogaster
910 gi1504040Homo Sapiens 4112 56
910 gi6273399Homo Sapiens AF200348_1 melanoma-4112 56
associated anti
en MG50
910 gi7292259Drosophila CG12002-PA 2388 36
melano aster
911 gi18175295Homo Sapiens CRB1 isofonn II 1258 28
precursor
911 gi18182323Mus musculus AF406641_1 crumbs-like1242 29
protein 1 precursor
911 gi29144951Mus musculus 5930402A21 protein4084 72
912 gi11493463Homo Sapiens AF130117 38 PR02852173 54
912 gi21104464Homo Sapiens OK/SW-CL.41 184 61
912 gi6650802Homo Sapiens AF118094 17 PRO1848200 56
913 gi6808611Homo sapiens AF204=231_1 88-kDa3237 99
Golgi
protein
913 gi6969980Homo sapicns AF163441 1 0l in 2345 98
67
913 gi7211438Homo Sapiens AF164622 2327 98
1 olgin-67
914 gi15030299Mus musculus _ 1881 94
protein kinase,
CAMP
dependent regulatory,
type I
beta
914 gi200365Mus musculus CAMP-dependent 1886 94
protein
kinase regulatory
subunit
914 gi307377Homo Sapiens CAMP-dependent 1957 99
protein
kinase RI-beta
regulatory
subunit
915 114017915Homo Sapiens I~IAA1849 protein 3460 100
915 17022002Homo Sapiens unnamed protein 3074 100
product
915 gi7022284Homo Sapiens unnamed protein 3460 100
product
916 gi1845577Mus musculus -lipoxygenase 2619 77
916 gi30047223Mus musculus Arachidonate lipoxygenase,2617 77
epidermal
916 gi3645913Mus musculus -lipoxygenase 2619 77
917 gi15489302Mus musculus arachidonate lipoxygenase,1142 69
epidermal
917 11845577Mus musculus -lipoxygenase 1139 69
917 gi30047223Mus musculus Arachidonate lipoxy1142 69
enase,
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TABLE 2 B
SEQ Hit ID Species Description S Percentage_
ID I scoredenti
epidermal
918 gi15489302Mus musculusarachidonate lipoxygenase,1263 75
epidermal
918 '1845577Mus musculus-lipoxygenase 1260 75
918 gi30047223Mus musculusArachidonate lipoxygenase,1263 75
epidermal
919 gi12053299Homo Sapienshypothetical protein2183 100
919 122478033Homo sa ienshypothetical protein3409 91
FLJ22944
919 gi22945612Drosophila CG31652-PA 131 23
melanogaster
920 gi14198207Mus musculushypothetical protein1599 98
BC008163
920 gi19343692Homo Sapiens 1625 100
920 gi7294965Drosophila CG4452-PA 615 40
melanogaster
921 gi21594983Homo Sapienscytokine-like protein238 74
C17
921 gi8132683Homo SapiensAF193766_1 cytokine-like238 74
protein C17
922 gi21594983Homo Sapienscytokine-like protein238 74
C17
922 gi8132683Homo SapiensAF193766_1 cytokine-like238 74
protein C 17
923 121594983Homo Sapienscytokine-like protein381 81
C17
923 gi8132683Homo SapiensAF193766_1 cytokine-like381 81
protein C17
924 gi21594983Homo Sapienscytokine-like protein263 98
C17
_ gi8132683Homo sapiensAF193766_1 cytolcine-like263 98
924 protein C17
925 gi21594983Homo sapienscytokine-like protein591 100
C17
925 gi8132683Homo SapiensAF193766_1 cytokine-like591 100
protein C17
926 gi13396317Homo Sapiens 2741 99
_ gi17975777Homo Sapiensvesicular inhibitory2741 99
926 amino acid
transporter
926 gi31566392Homo Sapiensvesicular inhibitory2741 99
amino acid
transporter
927 '22507470Mus musculusAI4134~81 protein 2042 92
927 gi3097285Rattus norvegicusZ~G 658 39
927 '802014 Rattus norvepreadipocyte factor653 39
icus 1
928 gi16768374Drosophila GM03282p 357 36
melanogaster
928 gi18088059Mus musculusE030025D05Rik protein1600 89
928 gi6624073Homo SapiensAC007743_1 similar 1755 93
to
hepatitis delta
antigen
interacting protein
A
929 gi14250638Homo SapiensAAH08783 Similar 864 97
to DNA
segment, Chr 17,
human
D6S54E
929 gi3941733Mus musculusAAC82476 BAT4 582 70
929 gi4337106Homo SapiensAAD18082 BAT4 864 97
930 gi27476065Oryza sativaPutative 266 30
(japonica phosphate/phosphoenolpyruvate
cultivar- translocator protein
group)
930 gi5911433Rattus norvegicusAF182714_1 putative621 88
phosphatelphosphoenolpyruvate
translocator
930 19759107Arabidopsis 282 30
thaliana
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TABLE 2 B
SEQ Hit_ID Species Description S Percentage_
ID I scoredenti
phosphate/phosphoenolpyruvate
translocator
protein-like
931 gi15277895Homosapiens AAH12939 1204 99
~ Similar
to
cardiotrophin-like
cytokine;
neurotrophin-1/B-cell
stimulating
factor-3
931 gi16356643Homo Sapiens cardiotrophin-like 1204 99
cytokine
931 gi6007643Homo Sapiens neurotrophin-1/B-cell 1204 99
stimulating
factor-3
932 gi18490933Homo Sapiens FLJ21269 846 98
protein
932 gi20268674Mus musculus MT-MC1 715 82
932 gi22003732Homo Sapiens AF527367_1 853 99
MTLC
933 gi15982236Mus musculus putative 1095 94
methionyl
aminopeptidase
933 gi23306398Arabidopsis , putative 744 50
thaliana
933 gi24899771Arabidopsis , putative 744 50
thaliana
934 gi1336013Mus musculus neurexophilin 550 45
2
934 gi22477181Homo Sapiens Similar 1649 99
to neurexophilin
4
934 gi4104963Rattus norvegicusneurexophilin 1493 90
4
935 gi12852913Mus musculus unnamed 193 75
protein
product
935 126326067Mus musculus unnamed 193 75
protein
product
937 gi19387136Homo Sapiens AF479748_1 874 99
PYRIN-
containing
APAF1-like
protein
5
937 gi202806Rattus norvegicusvasopressin 561 68
receptor
937 gi28436366Homo Sapiens NALP6 874 99
938 gi11321325Homo Sapiens AF311862 1030 100
1 Lin-7b
938 gi20381193Homo Sapiens Lin-7b protein; 1030 100
likely
ortholog
of mouse
LIN-7B;
mammalian
LIN-7 protein
2
938 gi3885828Rattus norvegicuslin-7-A 1019 98
939 gi14349125Homo Sapiens alpha2-glucosyltransferase 738 96
939 gi32490259~ry~,a sativa~SJNBb0116If07.1 190 36
japonica cultivar-
group)
939 13513451Rattus norvegicuspotassium 718 93
channel
regulator
1
940 113325140Homo Sapiens AAH04383 2693 100
940 gi35768Homo Sapiens polypirimidine 2693 100
tract binding
protein
940 gi35774~Homo Sapiens 2693 100
941 gi21522774Homo Sapiens unnamed product 3068 100
protein
941 gi24047224Homo Sapiens Similar 3048 99
to EGF-like-domain,
multiple
6
941 gi6752658Homo Sapiens AF186084_1 3043 99
epidermal
growth
factor repeat
containing
protein
942 gi21522772Homo Sapiens unnamed 3102 100
protein
product
942 gi24047224Homo sapiens Similar 3043 98
to EGF-like-domain,
multiple
6
942 gi6752658Homo Sapiens AF186084_1 3038 98
epidermal
growth
factor repeat
containing
protein
943 gi11385648Homo Sapiens AF273045_1 3867 99
C'TCL tumor
antigen
sel4-3
943 gi17980969Homo Sapiens AF454056_1 5146 99
sel4-3r
protein
943 gi29165763Mus musculus 3632413B07Rik 5213 82
protein
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TABLE 2 B
SEQ Hit Species Description S scorePercentage_
ID ID I denti
944 gi13677201Homo Sapiens 2771 100
944 gi17980969Homo Sapiens AF454056 1 sel4-3r3140 99
protein
944 gi29165763Mus musculus 3632413B07Rik protein3613 89
945 gi11385648Homo Sapiens AF273045_1 CTCL 3806 94
tumor
anti en sel4-3
945 gi17980969Homo Sapiens AF454056_1 sel4-3r5085 95
protein
945 gi29165763Mus musculus 3632413B07Rik protein5492 85
946 gi11385648Homo Sapiens AF273045_1 CTCL 3806 94
tumor
antigen sel4-3
946 gi17980969Homosapiens AF454056_1 sel4-3r5085 95
protein
946 gi29165763Mus musculus 3632413B07Rik protein5566 87
947 gi14043211Homo Sapiens AAH07594 Similar 2410 98
to RIKEN
cDNA 4931428F04
ene
947 '21739633Homo Sapiens hypothetical protein2430 97
947 '25058997Mus musculus 1110003N121Rik 941 63
protein
949 gi19387136Homo Sapiens AF479748_1 PYRIN- 1735 99
containing APAF1-like
protein
5
949 gi202806Rattus norve vasopressin receptor1030 64
'cus
949 gi28436366Homo Sapiens NALP6 1735 99
950 gi20338417Callus galluspotassium channel 5079 88
subunit
950 gi3875660Caenorhabditis 2164 45
ele ans
950 gi3978472Ratkus norvegicuspotassium channel 5376 90
subunit
951 gi18147612Homo Sapiens metalloprotease 4376 96
disintegrin
951 gi21908028Homo sapiens AF466287_1 a disintegrin4360 96
and
metalloprotease
domain 33
951 gi21908030Homo Sapiens a disintegrin and 4360 96
metalloprotease
domain 33
952 i 12841733Mus musculus unnamed protein 715 92
product
952 gi18606367Mus musculus RIKEN cDNA 4930570003715 92
952 gi31581976Homo sapiens FLJ20489 protein 472 100
953 gi154.20879Mus musculus AF398971_1 ankyrin204.9 83
repeat-
containing S~CS
box protein
10
953 gi18031949Mus musculus S~CS box protein 800 44
ASB-18
953 gi18092200Homo Sapiens AF417920_1 ASB-10 2174 91
954 gi32707Homo Sapiens interferon-omega 337 51
l
954 '386800Homo Sapiens interferon-alpha 340 51
954 1491284synthetic IFN-pseudo-ome 799 98
construct a 2
955 gi15928971Homo Sapiens AAH14951 Similar 430 90
to neuronal
thread protein
955 gi9844579Homo Sapiens 450 97
955 gi9844580Homo Sapiens 623 84
956 gi11559412Homo Sapiens NADPH-dependent 587 100
retinol
dehydrogenase/reductase
956 gi12804321Homo Sapiens AAH03019 peroxisomal685 100
short-
chain alcohol dehydrogenase
956 gi19113668Homosapiens NADP-dependentretinol878 100
dehydrogenase short
isoform
957 122658418Mus musculus cDNA sequence BC0309341499 68
957 gi28838433Homo Sapiens DI~FZp762A2013 1759 82
protein
957 gi30842594Homo Sapiens putative sulfhydryl1668 78
oxidase
precursor
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TABLE 2 B
SEQ Hit Species Description S Percentage_
ID ID I scoredenti
958 gi12958660Homo Sapiens AF321918_1 acid 2252 100
phosphatase
958 gi12958663Homo Sapiens AF321918 4 acid 1285 99
phosphatase
variant 3
958 gi52871Mus musculus lysosomal acid phosphatase832 45
959 gi11493443~Homo Sapiens AF130117 27 PR022091703 100
959 '28966 Homo Sapiens alpha 1-antitrypsin1703 100
959 gi6855601Homo Sapiens AF113676_1 PR00684 1703 100
960 gi11493443Homo Sapiens AF130117 27 PR022092040 95
960 gi177829Homo Sapiens alpha-1-antitrypsin2040 95
960 gi28966Homo Sapiens alpha 1-antitrypsin2040 95
961 il 1493443Homo Sapiens AF130117_27 PR022092025 95
961 gi177829Homo Sapiens alpha-1-antitrypsin2025 95
961 gi28966Homo Sapiens alpha 1-antitrypsin2025 95
962 gi11493443Homo Sapiens AF130117 27 PR022092036 95
962 1177829Homo Sapiens alpha-1-antitrypsin2036 95
962 gi28966Homo Sapiens alpha 1-antitrypsin2036 95
964 gi1841702Macaca fascicularisfertilin alpha-I 3138 70
isoform
964 gi2632092Pon o pygmaeusfertilin alpha protein4125 92
964 gi794073Macaca fascicularisfertilin alpha-I 3138 70
965 gi17887359Oryctolagus lipophilin AL2 248 54
cuniculus
965 gi4107229Homo Sapiens lipophilin A 454 100
965 gi4107231Homo Sapiens lipophilin B 267 60
966 gi13817037Homo Sapiens E-type ATPase 2812 99
966 gi20988653Homo Sapiens Similar to ectonucleoside2413 99
triphosphate
diphosphohydrolase
3
966 gi3335100Homo Sapiens CD39L3 2816 100
967 gi180251Homo sapiens precerebellin 542 57
967 16942096Mus musculus CBLN3 936 93
967 gi694209$Mus musculus AF218380 1 CBLN3 936 93
968 ' 18255724Mus musculus LOC215928 protein 131 28
968 gi21750370Homo Sapiens unnamed protein 1136 100
product
968 gi28460663Rattus norvegicusNa+ dependent glucose185 30
transporter 1
969 gi21750370Homo Sapiens unnamed protein 254.599
product
969 gi22328120Homo Sapiens hypothetical protein2077 99
DICFZp761N1114
969 gi26332881Mus musculus unnamed protein 2116 86
product
970 gi13161123Homo Sapiens AF332239_1 transcript147 54
Y 10
970 gi4545317Acipenser AF129437_1 immunoglobulin149 25
ruthenus light chain precursor
970 gi9937599Salmo trutta AF296378_1 MHC class153 31
I
heavy chain
971 gi12964746Mus musculus AF316612_1 neuronal2207 88
pentraxin receptor
971 gi2253263Rattus norvegicusneuronal pentraxin 2232 89
receptor
971 gi4160197Homo Sapiens 2512 99
972 gi27884137Danio rerio 3553 78
972 gi3170615Mus musculus DOC4 4166 96
972 gi4760782Mus musculus Ten-m4 4188 96
,
973 gi14714932Homo Sapiens AAH10623 -like 1 3770 100
973 121748606Homo sa iens FLJ00380 protein 372_996
973 gi541678Homo Sapiens hbZl7 3729 96
~
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TABLE 2 B
SEQ Hit_ID Species Description S Percentage_
ID I scoredenti
974 gi17044301Leishmania possible LIM-binding2875 36
major factor
974 gi23095182Drosophila CG13809-PA 3997 46
melanogaster
974 gi7716100Rattus norvegicusAF226993_1 selective8413 95
LIM
binding factor
975 gi20799661Mus musculus AF503575 1 mucolipin-21593 71
975 gi24417793Mus musculus mucolipin 2 1593 71
975 '24417795Homo Sapiens mucolipin 2 1912 86
976 '20799661Mus musculus AF503575_1 mucolipin-22394 83
976 gi24417793Mus musculus mucolipin 2 2394 83
976 gi24417795Homo Sapiens mucolipin 2 2817 99
977 gi1510147Homo sapiens 309 23
977 gi22477432Homo sapiens DI~F'ZP762N2316 4532 91
protein
977 gi403020,Mus musculus En-2/IacZ fusion 988 96
protein
980 gi1513059Homo sapieiisserin protease with2203 92
IGF-
binding motif
980 gi1621244Homo Sapiens novel serine protease,2203 92
PRSS11
980 gi5281519Homo Sapiens AF157623_1 HTRA 2203 92
serine
protease
981 gi11990126Camelus chymosin 1187 56
dromedarius
981 1540097Sus scrofa preprochymosin 1187 58
981 gi7008025Callithrix prochymosin 1346 64
jacchus
982 gi27356934Homo Sapiens extracellular sulfatase293 100
SULF-2
982 gi27356938Mus musculus extracellular sulfatase288 100
SULF-2
982 gi28191290Homo Sapiens sulfatase SULF1 276 68
precursor
984 gi27124671Homo Sapiens Zn-carboxypeptidase2008 99
984 gi27529696Paralichthys carboxypeptidase 808 4.9
olivaceus B
984 gi6013463Bothrops jararacacarboxypeptidase 817 46
homolo
985 gi27124671Homo Sapiens Zn-carboxypeptidase2008 99
985 gi27529696Paralichthys carboxypeptidase 808 49
olivaccus B
985 gi6013463Bothrops jararacacarboxypeptidase 817 46
homolog
986 '11545705Homo Sapiens ISCUl 663 99
986 gi11545707Homo Sapiens ISCU2 845 100
986 gi20381021Mus musculus Nifu-pendin protein807 96
987 gi12314022Homo Sapiens 883 89
987 gi22417143Homo Sapiens CGI-301 protein 853 100
987 gi32879760Homo Sapiens Snf7 homologue associated883 89
with Alix 1
988 gi12805221Mus musculus Lymphocyte antigen 137 33
6
complex, locus A
988 gi198924.Mus musculus Ly-6A.2 137 33
988 gi201113Mus musculus T-cell activation 137 33
protein
989 gi17512406Mus musculus differential display1063 67
and
activated by p53
989 gi25166615Homo Sapiens AF223000_1 DDA3-like1673 99
protein
989 gi25166621Homo Sapiens AF322891_1 DDA3-like1673 99
protein
990 gi15990480Homo Sapiens -binding protein 1570 100
2
990 gi21961217Homo Sapiens -binding protein 1570 100
2
990 122213050Mus musculus B230313N05Rik protein1555 98
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TABLE 2 B
SEQ Hit Species Description S Percentage_
ID ID I scoredenti
991 gi204058Rattus norvegicusextracellular signal-related1497 62
kinase 3
991 gi23903Homo Sapiens 63kDa protein kinase2894 99
991 gi27882123Danio rerio Similar to mitogen-activated1670 61
protein kinase 4
992 gi17016967Homo Sapiens AF435011 1 NUANCE 5643 97
992 gi17861384Homo Sapiens nesprin-2 gamma 5643 97
992 gi24417711Homo Sapiens nesprin-2 5643 97
993 gi18204756Musmusculus 2310044D20Rikprotein626 68
993 gi21706580Mus musculus A830073021Rik protein170 29
993 gi33328302Homo Sapiens NS5ATP6 997 100
994 gi19353133Mus musculus Clq-like 961 66
994 gi26996600Mus musculus Similar to Clq-like1468 94
994 gi32401227Homo Sapiens AF525315_1 Clq-domain1528 98
containing protein
995 gi14718648Homo Sapiens allantoicase 1633 99
995 gi20987689Homo Sapiens Similar to allantoicase1838 99
995 gi9255889Mus musculus AF278712 1 allantoicase1465 77
996 115617341Homo Sapiens LAG-3 protein precursor2813 99
996 gi30851187Homo Sapiens LAG3 protein 1906 99
996 gi579596Homo Sapiens lymphocyte protein 2651 98
997 gi13810285Rattus norvegicusguanine nucleotide 5813 91
release/exchange
factor
997 gi2522208Homo sapiens Ras-GRF2 6407 99
997 gi5882290Homo sapiens Ras guanine nucleotide6401 99
exchange factor
2
998 gi22038159Homo Sapiens AF527605_1 ~iziminl8544 100
998 gi28374~168Mus musculus AA959601 protein 8001 92
998 gi31419757Mus musculus AA959601 protein 8001 92
999 gi10433672Homo Sapiens unnamed protein 1530 100
product
999 gi19263505Homo Sapiens hypothetical protein1530 100
FLJ12242
999 gi23272394Homo Sapiens KCTI~2 protein 728 67
1000 gi14~04~1697Homo Sapiens 3585 99
1000 121594273Homo Sapiens 3626 100
1000 gi25303955Homo Sapiens 3600 100
1001 gi1438532Rattus norvegicusrAl 527 25
1001 gi1438534Rattus norvegicusrA9 4640 67
1001 gi27371336Homo Sapiens Similar to CTD-binding2008 97
SR-
like protein rA9
1002 gi1438534Rattus norvegicusrA9 4640 67
1002 gi27371336Homo sapiens Similar to CTD-binding2008 97
SR-
like protein rA9
1002 gi7296722Drosophila CG2926-PA 536 23
melanogaster
1003 gi1675220Cricetulus SREBP cleavage activating6194 92
griseus protein
1003 gi23240172Drosophila CG33131-PA 1077 32
melanogaster
1003 gi30048445Mus musculus Similar to SREBP 2600 89
CLEAVAGE-ACTIVATING
PROTEIN
1004 gi12652851Homo Sapiens AAH00178 potassium 1987 100
channel
modulatory factor
1004 gi26453336Homo sapiens FIGC1 1983 99
~
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TABLE 2 B
SEQ Hit Species Description S Percentage_
ID ID I scoredenti
1004 gi7677058Homo Sapiens AF155652_1 potassium1983 99
channel modulatory
factor
1005 gi26341968Mus musculus unnamed protein 654 54
product
1005 gi27695389Mus musculus MGC58017 protein 1058 98
1005 130481648Homo Sapiens 654 54
1006 gi11875318Mus musculus synaptotagmin XIII 2004 89
1006 gi14210274Rattus norvegicusAF375466_1 synaptotagmin2000 89
13
1006 gi21410154Mus musculus synaptotagmin 13 2004 89
1007 gi11342591Mus musculus RanBP7/importin 5415 99
7
1007 gi32330683Mus musculus importin 7 5427 99
1007 gi3800881Homo Sapiens RanBP7limportin 5447 100
7
1008 gi17939650Homo Sapiens AAH19302 hypothetical3770 99
protein FLJ12525
1008 gi18676522Homo Sapiens FLJ00158 protein 1512 100
1008 127462078Homo Sapiens AF116730_1 MSTP060 3739 96
1009 gi28981429Mus musculus Ddefl protein 4690 95
1009 gi4063614Mus musculus ADP-ribosylation 4701 94
factor-
directed GTPase
activating
protein isoform
a
1009 gi4406393Bos taurus differentiation 4700 95
enhancing factor
1
1011 113872813Homo Sapiens fibulin-6 541 29
1011 ' 14575679Homo Sapiens AF156100 1 hemicentin537 29
1011 gi92804.05Homo Sapiens AF245505_1 adlican 1631 47
1012 gi1284.3704Mus musculus unnamed protein 1005 72
product
1013 gi12833251Mus musculus unnamed protein 710 58
product
1013 gi17511816Homo Sapiens AAH18758 Similar 1468 99
to RII~EN
cDNA 1110032022
gene
1013 gi20071678Mus musculus 710 58
1014 gi12833251Mus musculus unnamed protein 748 65
product
1014 gi17511816Homo Sapiens AAH18758 Similar 1288 90
to RIKEN
cDNA 1110032022
gene
1014. gi20071678Mus musculus 74=8 65
1015 gi13529248Homo Sapiens Centrin 3 839 99
1015 gi2246401Homo Sapiens centrin 842 100
1015 gi30582215Homo Sapiens 839 99
1016 gi31455256Homo Sapiens IMAGE3510317 protein2496 100
1016 132492907Homo Sapiens selenoprotein ~ 2496 100
1016 16572230Homo Sapiens 1879 99
1017 gi31455256Homo Sapiens IMAGE3510317 protein2142 100
1017 gi32492907Homo sapiens selenoprotein ~ 2142 100
1017 gi6572230Homo Sapiens 3997 99
1018 gi21928729Homo Sapiens seven transmembrane2190 99
helix
receptor
1018 gi6693701Homo Sapiens AF147788 1 melanopsin2226 91
1018 gi6693703Mus musculus AF147789_1 melanopsin1729 74
1019 gi20072741Mus musculus E430025L02Rik protein2634 80
1019 gi28380382Drosophila CG4168-PA 309 29
melanogaster
1019 gi439296Homo Sapiens garp 793 37
1020 gi15487302Homo Sapiens medium-chain acyl-CoA1346 99
synthetase
1020 gi15706421Homo Sapiens middle-chain acyl-CoA1346 99
synthetase 1
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TABLE 2 B
SEQ Hit ID Species Description S Percentage_
ID score
I denti
1020 gi5019275Bos taurus xenobiotic/medium-chain1088 78
fatty
acid:CoA ligase
form XL-III
1021 gi18874700Homo SapiensAF478469_1 Rapl 5803 98
guanine
nucleotide-exchange
factor
PDZ-GEF2B
1021 gi20386206Homo SapiensAF478567_1 PDZ domain-5822 98
containing guanine
nucleotide
exchange factor
PDZ-GEF2
1021 gi6650766Homo SapiensAF117947_1 PDZ domain-6216 100
containing guanine
nucleotide
exchange factor
I
1022 gi18874698Homo SapiensAF478468_1 Rapl 5923 99
guanine
nucleotide-exchange
factor
PDZ-GEF2A
1022 gi18874700Homo SapiensAF478469_1 Rapl 5923 99
guanine
nucleotide-exchange
factor
PDZ-GEF2B
1022 gi20386206Homo SapiensAF478567_1 PDZ domain-5942 100
containing guanine
nucleotide
exchange factor
PDZ-GEF2
1023 gi13810306Homo Sapienstransmembrane protein261 37
7
1023 ' 18250724Mus musculustransmembrane protein257 36
7
1023 gi20270907OncorhynchusAF483531_1 'IHSV-induced233 33
mylciss protein-5
1024 gi20071315Mus musculusAA589509 protein 1116 76
1024 gi21779866Mus musculusAF458068_1 IL-17RE 2052 66
1024 gi21779869Homo SapiensAF458069_1 IL-17RE 2896 100
1025 120071315Mus musculusAA589509 protein 1116 76
1025 gi21779866Mus musculusAF458068_1 IL-17RE 2028 72
1025 gi21779869Homo SapiensAF458069_1 IL-17RE 2928 100
1026 gi14150450Rattus norvegicusAF241241_1 UDP- 1350 93
GalNAc:polypeptide
N-
acetylgalactosaminyltransferase
T9
1026 gi25809274Homo Sapienspolypeptide N- 1390 97
acetylgalactosaminyltransferase
10
1026 gi28268676Homo SapiensUDP-N-acetyl-alpha-D-1384 96
galactosamine:polypeptide
N-
aeetylgalactosaminyltransferase
10
1027 gi15217067Homo SapiensAF400436_1 stem 1019 95
cell factor
isoform 1
1027 gi1827477Felis catus stem cell factor 896 84
1027 gi337934Homo sapiensstem cell factor 1019 95
1028 gi1377895Homo SapiensOB-cadherin-2 1572 56
1028 gi30171995Homo Sapienscadherin-24 2721 93
1028 gi30171998Homo Sapienscadherin-24 variant2987 99
1029 gi1377895Homo SapiensOB-cadherin-2 1621 60
1029 gi30171995Homo Sapienscadherin-24 2770 99
1029 '30171998Homo Sapienscadherin-24 variant2721 93
1030 gi1398903Mus musculusCa2+ dependent activator6763 94
protein for secretion
1030 gi21541504Homo SapiensAF458662_1 calcium-6440 93
dependent activator
protein for
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TABLE 2 B
SEQ Hit ID Species Description S scorePercentage-
ID Identi
secretion protein
1030 gi577428Rattus norvegicusCa2+-dependent 6449 93
activator
protein; calcium-dependent
actin-binding protein
1031 gi11071729Homo Sapiens putative dipeptidase1847 99
1031 gi11125344Homo Sapiens putative metallopeptidase1319 72
1031 gi32490515Mus musculus putative membrane-bound1313 71
dipeptidase-3
1032 gi11493652Homo Sapiens AF200708 1 calcium2552 100
channel
blocker resistance
protein
CCBR1
1032 gi13924720Homo Sapiens AF252872_1 cystine/glutamate2552 100
transporter xCT
1032 gi15082352Homo Sapiens AAH12087 member 2552 100
11
1033 gi17028348Homo sapiens DKFZP586G1517 protein3748 100
1033 gi20987924Mus musculus 2410004L15Rik protein3473 92
1033 gi29612455Mus musculus 2410004L15Rik protein3807 92
1034 gi19352987Homo sapiens Similar to KIAA04336348 98
protein
1034 gi2887437Homo Sapiens KIAA0433 6487 99
1034 gi31418648Mus musculus 4981 97
1035 gi11066463Rattus norvegicusAF225961_1 RhoGEF 6385 80
glutamate transport
modulator
GTRAP48
1035 gi19387126Mus musculus AF467766_1 guanine1778 33
nucleotide exchange
factor
1035 gi7110160Homo Sapiens guanine nucleotide1792 38
exchange
factor
1036 gi10726794Drosophila CG5521-PA 508 35
melanogaster
1036 gi24061707Mus musculus GAP-related interacting986 97
partner
to E12
1036 gi4240257Homo Sapiens KIAA0884 protein 2491 100
1037 gi20269957Sus scrofa AF4.98759_1 phospholipase1472 85
C
delta 4.
1037 gi21307610Mus musculus phospholipase C 1327 77
delta 4
1037 gi571466Rattus norvegicusphospholipase C 1295 76
delta-4
1038 gi16552885Homo Sapiens unnamed protein 2084 99
product
1038 gi26326051Mus musculus unnamed protein 1085 54
product
1038 gi26327387Mus musculus unnamed protein 1085 54
product
1039 118480186Mus musculus olfactory receptor1323 81
M~R261-6
1039 gi32052343Mus musculus olfactory receptor1323 81
GA_x6K02T2P3E9-4384160-
4383228
1039 19368991Homo Sapiens 14.10 100
1040 gi29791964Homo Sapiens Thrombospondin 4798 99
4
1040 gi311626Homo Sapiens thrombospondin-4 4787 99
1040 gi3860231Mus musculus thrombospondin-4 4557 93
1041 gi14043083Homo Sapiens AAH07524 sperm 660 100
associated
antigen 9
1041 gi24460121Homo Sapiens AF327452_1 JNK-associated273 98
leucine-zipper
protein
1041 gi29169179Homo Sapiens PHET 343 98
1042 gi21654741Homo Sapiens peptide/histidine 2771 95
transporter
1042 gi2208839Rattus norvegicuspeptide/histidine 2344 82
transporter
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TABLE 2 B
SEQ Hit Species Description S Percentage_
ID ID I scoredenti
1042 gi33126130Homo Sapiens peptide/histidine 2736 94
transporter
1043 gi22831474Drosophila CG14622-PC 2508 47
melanogaster
1043 gi22831475Drosophila CG14622-PB 2508 47
melanogaster
1043 gi29477075Mus musculus Similar to dishevelled2521 93
associated activator
of
morphogenesis 1
1044 gi15929979Homo Sapiens AAH15418 Similar 2476 100
to zinc
fin er protein 345
1044 gi33417243Mus musculus B230312I18Rik protein1788 57
1044 gi5080758Homo Sapiens AC007842 3 BC331191_11922 52
1045 gi12655913Homo Sapiens AF227516 1 sprouty-4A386 98
1045 gi12655915Homo Sapiens AF227517 1 sprouty-4C386 98
1045 gi29747900Mus musculus Sprouty homolog 320 81
4
1046 gi29692498Mus musculus NAAG-peptidase II 3447 88
1046 gi3211746Sus scrofa folylpoly-gamma-glutamate2819 70
carboxypeptidase
1046 gi4539525Homo Sapiens NAALADase II protein3881 100
1047 gi21750009Homo Sapiens unnamed protein 1414 99
product
1047 gi23512248Homo Sapiens Similar to DISC~ 676 53
Interacting
Protein 2
1047 gi26449269Maraca fasciculariShypothetical protein1421 99
1048 15918167Homo Sapiens plexin-B1/SEP receptor3578 42
1048 16651051Mus musculus AF133093 2 plexin 3147 40
6
1048 19885259Homo Sapiens AF149019 1 plexin-B33140 40
1049 gi15081392Homo Sapiens AF395817 1 NAC1 1268 55
protein
1049 gi30931339Musmusculus Nacl-pending protein1254 57
1049 gi33392751Homo Sapiens NAC1 protein 1268 55
1050 gi11692802Homo Sapiens AF320294_l ABCG8 3123 99
1050 ' 15088540Homo Sapiens AF324494 1 sterolin-23127 99
1050 115146444Homo Sapiens AF351824~ 1 sterolin-23117 99
1051 gi12652851Homo Sapiens AAH00178 potassium 1987 100
channel
modulatory factor
1051 gi26453336Homo Sapiens FIGC1 1983 99
1051 gi7677058Homo Sapiens AF155652_1 potassium1983 99
channel modulatory
factor
1052 gi33395Homo Sapiens 703 70
1052 gi33730Homo Sapiens immunoglobulin lambda716 71
light
chain
1052 gi33734Homo Sapiens immunoglobulin lambda716 71
light
chain
1053 gi21388773Homo Sapiens kringle-containing 1764 80
protein
1053 gi21388775Homo Sapiens kringle-containing 1453 78
protein
1053 gi21623530Homo Sapiens kringle-containing 1458 68
transmembrane protein
1054 gi14495324Homo Sapiens CMRF35A 432 48
1054 gi18490143Homo Sapiens CM12F35 leukocyte 432 48
immunoglobulin-like
receptor
1054 gi396170Homo Sapiens CMRF-35 antigen 432 48
1055 gi4468255Homo Sapiens MHC class I antigen1925 98
1055 gi4468256Homo Sapiens MHC class I antigen1974 100
1055 gi487909Homo Sapiens HLA-Al l antigen 1914 97
Al 1.1
1056 gi21667214Homo Sapiens AF465767 1 741 100
~ ~
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TABLE 2 B
SEQ Hit Species Description S Percentage_
ID ID _ I scoredenti
bactericidal/permeability-
increasing protein-like
3
1056 gi32490539Homo Sapiens RY2G5 171 32
1056 gi57732Rattus rattuspotential ligand-binding210 35
protein
1057 gi21667214Homo Sapiens AF465767_1 2223 99
bactericidal/permeability-
increasing protein-like
3
1057 132490539Homo Sapiens RY2G5 524 31
1057 gi57732Rattus rattuspotential ligand-binding564 32
protein
1058 gi21667214Homo Sapiens AF465767_1 1916 99
bactericidal/permeability-
increasing protein-like
3
1058 gi32490539Homo Sapiens RY2G5 434 31
1058 gi57732Rattus rattuspotential ligand-binding473 33
protein
1059 gi21667214Homo Sapiens AF465767_1 1842 100
bactericidal/permeability-
increasing protein-like
3
1059 gi32490539Homo Sapiens RY2G5 434 31
1059 gi57732Rattus rattuspotential ligand-binding473 33
protein
1060 gi13529158Homo Sapiens AAH05349 1128 99
1060 i529514~Sus scrofa neuronal endocrine 1092 95
protein
1060 17718079Homo Sapiens neuroendocrine protein1148 100
7B2
1061 gi15929030Homo Sapiens AAH14973 2325 100
1061 gi16551493Homo Sapiens unnamed protein 2321 99
product
1061 gi18698601Homo Sapiens AF467443_1 Smith-Magenis2325 100
syndrome chromosome
region
candidate 7 protein
1062 gi13543081Mus musculus claudin 6 822 70
1062 gi4128041Homo sapienS claudin-9 protein 1116 100
1062 gi4325296Mus muSCUlus olaudin-9 1078 95
1063 gi 121574.2Homo Sapiens HIP 434 65
1063 gi14286258Homo Sapiens AAH08926 ribosomal 434 65
protein
L29
1063 gi793843Homo Sapiens ribosomal protein 434 65
L29
1064 gi4587895Rattus norvegicusAF072509_1 glutamate3549 86
receptor interacting
protein 2
1064 gi4731287Rattus norvegicusglutamate receptor 3281 81
interacting
protein 2
1064 gi6601555Rattus norvegicusglutamate receptor 3549 86
interacting
protein 2
1065 gi23496442Rattus norvegicusdisabled-1 2807 96
1065 gi3288852Homo Sapiens disabled-1 2865 99
1065 gi8118615Homo Sapiens AF263547_1 disabled-12842 99
1066 gi16877456Homo Sapiens AAH16974 1711 100
1066 gi20810324Homo Sapiens 1410 86
1066 gi26351033Mus musculus unnamed protein 1236 76
product
1067 gi15430703Homo Sapiens AF362953_1 testis 1858 99
specific
serine/threonine
kinase 2
1067 gi2738898Mus musculus protein kinase 1683 89
1067 gi33590489Rattus norvegicusserine/threonine 1754 92
kinase 22B
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TABLE 2 B
SEQ Hit ID Species Description S scorePercentage_
ID Identi
1068 gi12963879Homo Sapiensprostaglandin D 980 96
synthase
1068 gi13543568Homo SapiensPTGDS protein 980 96
1068 gi189772Homo Sapiensprostaglandin D2 980 96
synthase
1069 gi14336718Homo sapiensAE006464_18 similar1157 100
to
HAGH
1069 gi20988885Mus musculus2810014I23Rik protein1153 79
1069 gi2459803Rattus norvegicusRSP29 645 48
1070 gi13397835Homo Sapiensannexin A13 isoform1795 99
b
1070 gi21218387Oryctolagus AF510726_1 annexin 1589 88
cuniculus XIIIb
1070 gi757784Canis familiarisannexin XIIIb 1621 89
1071 gi204222Rattus norvegicusGABA transporter 3094 96
protein
1071 gi21707908Homo Sapiens, member 1 3126 98
1071 gi31658 Homo SapiensGABA transporter 3111 98
1072 gi14165176Rattus norvegicusAF378093_1 sodium 823 98
channel
beta 3 subunit
1072 gi7160975Homo Sapiensvoltage-gated sodium834 100
channel
beta-3 subunit
1072 gi7161889Rattus norvegicusvoltage-gated sodium823 98
channel
beta-3 subunit
1073 gi20381266Homo SapiensGlypican 2 3040 100
1073 gi440127Rattus norvegicuscerebroglycan 2506 82
1073 gi5911320Mus musculusAF105268_1 glypican-61164 44
1074 gi18676470Homo SapiensFLJ00132 protein 2515 99
1074 gi19344068Mus musculus2700038E08Rik protein3407 77
1074 gi23274106Mus musculus2700038E08Rik protein3407 77
1075 gi25396387Homo Sapiensalpha 2,6-sialyltransferase_ 100
2844
1075 gi27650880Homo Sapiensbeta-galactoside 1183 100
alpha-2,6-
sialyltransferase
1075 gi452751Gallus gallusGal beta 1,4 GIcNAc943 54
alpha 2,6-
sialyltransferase
1076 gi13344995Homo SapiensCat Eye Syndrome 2002 99
critical
region protein isoforna
1
1076 gi 13344997Homo SapiensCat Eye Syndrome 2223 100
critical
region protein isoform
2
1076 gi27503696Homo SapiensSimilar to cat eye 2223 100
syndrome
chromosome region,
candidate
5
1077 gi13344995Homo SapiensCat Eye Syndrome 1662 96
critical
region protein isoform
1
1077 gi13344997Homo SapiensCat Eye Syndrome 1662 96
critical
region protein isoform
2
1077 gi27503696Homo SapiensSimilar to cat eye 1662 96
syndrome
chromosome region,
candidate
5
1078 gi177870Homo Sapiensalpha-2-macroglobulin2718 39
precursor
1078 '25303946Homo Sapiensalpha-2-macro lobulin2718 39
1078 1579592 Homo Sapiensal ha 2-macroglobulin2712 39
690-730
1079 gi25303946Homo Sapiensalpha-2-macroglobulin1290 35
1079 gi579592Homo Sapiensalpha 2-macroglobulin1290 35
690-730
1079 gi579594Homo Sapiensalpha 2-macroglobulin_ 36
690-740 1291
1080 gi25303946Homo Sapiensalpha-2-macroglobulin761 31
~ 1080gi671864Gallus gallusovomacroglobulin, _ 32
~ ~ ~ ovostatin ~ 792
~
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TABLE 2 B
SEQ Hit ID Species Description S Percentage_
ID I scoredenti
1080 gi671865Gallus gallusovomacroglobulin, 792 32
ovostatin
1081 gi177870Homo sapiensalpha-2-macroglobulin2736 39
precursor
1081 gi25303946Homo Sapiensalpha-2-macroglobulin2736 39
1081 gi579592Homo sapiensalpha 2-macroglobulin2730 39
690-730
1082 gi25303946Homo Sapiensalpha-2-macroglobulin1290 35
1082 gi579592Homo Sapiensalpha 2-macroglobulin1290 35
690-730
1082 gi579594Homo Sapiensalpha 2-macroglobulin1291 36
690-740
1083 gi17512361Mus musculusesterase 31 2029 66
1083 '29476863Mus musculusSimilar to esterase2022 66
31
1083 '404389 Mus sp. carboxylesterase; 2001 66
Es-male
1084 gi207286Rattus norvegicusTGF-beta masking 8721 89
protein
large subunit
1084 gi26006334Mus musculuslatent transforming8630 88
growth
factor beta binding
protein 1L
1084 gi3493176Mus musculuslatent TGF beta 8627 88
binding protein
1085 117985371Homo SapiensI3 binding protein 861 100
1085 gi18466808Homo SapiensAF283671_1 cervical853 99
cancer 1
proto-oncogene-binding
protein
I~G19
1085 gi21961229Homo SapiensBRI3 binding protein861 100
1086 gi222833Gallus gallusM-protein 2924 42
1086 i295034~7Mus musculusM-protein 2908 42
1086 gi407097Homo Sapiens165kD protein 2912 42
1087 gi12655165Homo sapiensAAH01438 zinc finger693 65
protein
256
1087 gi30582545Homo Sapienszinc finger protein693 65
256
1087 gi4894364Homo Sapiens1~F067165_1 zinc 693 65
finger
protein 3
1088 gi1613848Homo Sapienszinc finger protein311 49
zfp6
1088 130582545Homo Sapienszinc finger protein309 56
256
1088 gi4894364Homo SapiensAF067165_1 zinc 309 56
finger
protein 3
1089 112655452Homo Sapienslematin associated 981 76
protein 4.7
1089 gi 12655460Homo Sapienskeratin asSOCiated 970 77
protein 4.12
1089 112655464Homo sapienskeratin associated 973 81
protein 4.15
1090 gi12655446Homo sapienskeratin associated 400 69
protein 4.4
1090 112655452Homo Sapienskeratin associated 383 81
protein 4.7
1090 gi12655460Homo Sapienskeratin associated 400 61
protein 4.12
1091 gi12655452Homo Sapienskeratin associated 1219 90
protein 4.7
1091 gi12655460Homo Sapienskeratin associated 1158 88
protein 4.12
1091 gi 12655464Homo Sapienskeratin associated 1260 100
protein 4.15
1092 gi15722084Homo Sapiens 1991 100
1092 gi434306Homo Sapienslysosomal acid lipase;1289 63
sterol
esterase
1092 '506431 Homo sapienslysosomal acid lipase1289 63
1093 115722084Homo Sapiens 1935 100
1093 gi434306Homo Sapienslysosomal acid lipase;1289 63
sterol
esterase
1093 gi506431Homo Sapienslysosomal acid lipase1289 63
1094 gi20152322Homo sapiensputative G-protein 1558 99
coupled
receptor
1094 gi32526601Homo SapiensGPRCSD 1558 99
1094 gi8118040Homo Sapiens~ AF209923 1 orphan~ ~ 99
G-protein 1804
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TABLE 2 B
SEQ Hit_ID Species Description S scorePercentage_
ID I denti
coupled receptor
1095 gi15099951Mus musculusAF384160_1 diacylglycerol596 49
acyltransferase
2
1095 gi18129609Homo SapiensAF384161_1 diacylglycerol597 49
acyltransferase
2
1095 gi27693972Mus musculusdiacylglycerol O- 596 49
acyltransferase
2
1096 gi17224598Homo SapiensAF293615_1 blood 1134 95
dendritic
cell antigen 2 protein
_1096 gi17225337Homo SapiensAF325459_1 dendritic1134 95
lectin
1096 gi17225339Homo SapiensAF325460_1 dendritic930 80
lectin b
isoform
1097 gi17224598Homo SapiensAF293615_1 blood 1182 99
dendritic
cell antigen 2 protein
1097 117225337Homo SapiensAF325459_1 dendritic1182 99
lectin
1097 gi17225339Homo SapiensAF325460_1 dendritic978 84
lectin b
isoform
1098 gi18479834Mus musculusolfactory receptor 1220 77
MOR144-1
1098 gi21929119Homo Sapiensseven transmembrane1595 100
helix
receptor
1098 gi32063297Mus musculusolfactory receptor 1220 77
GA_x6K02T2PVTD-
14025733-14026668
1099 gi19526645Homo SapiensAF430017_1 intestinal775 33
membrane mucin MUC17
1099 gi5911169Homo SapiensAF147790_1 transmembrane3049 99
mucin 12
1099 gi5911171Homo SapiensAF147791_1 mucin 671 54
11
1100 gi219497Homo sapiensbiliary glycoprotein446 34
1100 gi3172151Homo SapiensBGP _HUMAN 446 34
1100 gi37198 Homo SapiensTM1-CEA preprotein 446 34
1101 gi1504040Homo Sapiens 4709 60
1101 gi6273399Homo SapiensAF200348_1 melanoma-4709 60
associated antigen
MG50
1101 gi7292259DroSOphila CCa12002-PA 2660 38
melanogaster
1102 gi1504040Homo sapiens 4596 59
1102 gi6273399Homo sapiensAF200348_1 melanoma-4596 59
associated antigen
MG50
1102 gi7292259Drosophila CG12002-PA 2606 38
melanogaster
1103 ' 10435776Homo Sapiensunnamed protein 4413 99
product
1103 '11611734Homo SapiensAF245388_1 GREBla 510 46
1103 17264653Mus musculusAF180470 1 I~iaa05753121 53
1104 gi16519041Drosophila AF427496_1 occludin-like184 23
melanogasterprotein
1104 gi20219008ChlamydomonasAF394181_1 coiled-coil673 36
reinhardtii flagellar protein
1104 gi7301551Drosophila CG6059-PA 169 19
melanogaster
1105 gi 12654511Homo SapiensTorsin family 3, 693 96
member A
1105 gi 14043167Homo SapiensTorsin family 3, 693 96
member A
1105 gi 15079904Homo SapiensTorsin family 3, 693 96
member A
1106 gi21666374Mus musculusswan 325 72
~ 1106gi21666376Mus musculusswan 325 72
~ ~
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TABLE 2 B
SEQ Hit ID Species Description S scorePercentage-
ID Identi
1106 gi29747798Mus musculus3000004N20Rik protein704 86
1107 gi15076843Homo SapiensAF233450_1 pecanex-like2759 68
protein 1
1107 118157547Mus musculusAF237953_1 pecanex-like4201 93
3
1107 16650377Mus musculusAF096286_1 pecanex 2767 67
1
1108 gi15076843Homo SapiensAF233450_1 pecanex-like2402 73
protein 1
1108 '18157547Mus musculusAF237953 1 pecanex-like3138 97
3
1108 16650377Mus musculusAF096286 1 pecanex 2406 73
1
1109 gi21595759Homo Sapienssimilar to HC6 211 71
1109 gi7020440Homo Sapiensunnamed protein 215 57
product
1109 gi7770237Homo SapiensAF119917_62 PR02822232 61
1110 gi26333913Mus musculusunnamed protein 749 83
product
1110 '26343633Mus musculusunnamed protein 749 83
product
1110 gi27370621Homo sapiensSimilar to hypothetical828 95
protein
FLJ31737
1111 gi12043567Homo sapiensunc-93 related protein1571 99
1111 gi17390915Mus musculusunc93 homolo B 1367 87
1111 gi23271746Mus musculusUnc93b protein 1367 87
1112 gi15990461Homo SapiensAAH15612 ring finger2465 100
' protein
25
1112 gi18490513Mus musculusRnf25 protein 1983 82
1112 gi29179411Mus musculusRing finger protein1988 82
25
1113 gi19716048Xenopus laevisWeelB kinase 1123 45
1113 gi2827996Xenopus laevisweel homolog 1291 51
1113 gi644770Xenopus laevisVVeelA kinase 1296 51
1115 gi15030119Mus musculus3110057O12Rik protein777 97
1115 gi23093574.Drosophila CG32112-PA 366 42
melanogaster
1115 gi23093575Drosophila CG32112-PB 397 47
melanogaster
1116 gi114.93409Homo sapiensAF130117 10 PR00898129 59
1116 gi21708029Homo Sapienssimilar to Alu subfamily135 70
S(~l
sequence contamination
warning entry
1116 gi28800991Homo Sapiensunnamed protein 124 67
product
1117 gi13810898Rattus norvegicusAF322216_1 inhibin 515 32
binding
protein long isoform
1117 gi2370143Homo Sapiensimmunoglobulin-like503 32
domain-
containin 1
1117 gi2645890Homo sapiensIGSF1 503 32
1118 gi2370143Homo Sapiensimmunoglobulin-like307 38
domain-
containin 1
1118 gi32330685Mus musculusinhibin binding 310 38
protein/p120
long isoform
1118 gi32330691Mus musculusinhibin binding 310 38
protein/p120
variant 4
1119 gi21595190Mus musculus2510001A17Rile protein4878 95
1119 gi21707128Homo sapiensRan binding protein5047 99
11
1119 gi6650612Homo SapiensAF111109_1 Ran binding5047 99
protein 11
1120 11399805Homo SapiensBbp/53BP2 2078 46
1120 116197705Homo SapiensASPP2 protein 2439 47
1120 gi18652832Homo Sapiens~ ASPP1 protein ~ 5703~ 99
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TABLE 2 B
SEQ Hit ID Species Description S Percentage_
ID score
I denti
1122 gi2598461Homo Sapiens 1893 97
1122 gi31418316Homo SapiensHeat shock 70kD 1893 97
protein
binding protein
1122 gi4049268Homo sapiensputative tumor suppressor1893 97
ST13
1123 gi11991844Homo SapiensAF243505_1 fibrocyte-derived676 100
protein
1123 gi 12619173Homo Sapiensmelanoma inhibitory676 100
activity
like protein
1123 gi 12668328Homo Sapiensmelanoma inhibitory676 100
activity
like protein
1124 gi22760096Homo Sapiensunnamed protein 1047 89
product
1124 gi27883913Homo SapiensPOTE 525 46
1124 gi28279813Homo SapiensSimilar to hypothetical743 85
protein
DKFZp434A 171
1125 gi11990779Homo Sapiens 548 43
1125 gi22760096Homo Sapiensunnamed protein 831 87
product
1125 gi28279813Homo SapiensSimilar to hypothetical743 85
protein
DKFZp434A 171
1126 gi11493483Homo SapiensAF130117_48 PRO2550265 67
1126 gi1872200Homo Sapiensalternatively spliced259 66
product
using exon 13A
1126 gi7770139Homo sapiensAF119917 13 PRO1722266 60
1128 gi16588454Homo sapiensAF312374 1 A(~TRAP 708 95
protein
1128 gi16878260Homosapiens AAH17328 Similar 726 100
to
angiotensin II,
type I receptor-
associated protein
1128 gi9621816Homo sapiensAF165187 1 ATRAP 708 95
1129 gi12330704Mus musculusAF333770_l cell 1376 71
recognition
molecule CASPR4
1129 gi17986216Homo SapiensAF333769_1 cell 1864 98
recognition
molecule CASPR3
1129 121961652Mus musculuscontactin associated1376 71
protein 4
1130 gi17986216Homo SapiensAF333769_1 cell 6812 99
recognition
molecule CASPR3
1130 gi18390059Homo sapiensAF463518_1 cell 4738 70
recognition
protein CASPR4
1130 gi21961652Mus musculuscontactin associated4709 68
protein 4
1131 gi10336504Homo SapiensUDP-CaalNAc: polypeptide2014 61
N-
acetylgalactosaminyltransferase
1131 gi21552746Homo SapiensAF410457_1 putative3157 99
polypeptide N-
acetyl alactosaminyltransferase
1131 gi21552969Mus musculusAF467979_1 Williams-Beuren3098 97
syndrome critical
region gene
17
1132 gi13625176Homo SapiensAF251057_1 thrombospondin575 46
1132 gi18490857Homo SapiensThrombospondin 575 46
1132 gi31127148Mus musculus2610028F08Rik protein860 96
1133 gi11907599Homo SapiensAF208291_1 protein 857 50
kinase
HIPI~2
1133 gi5305331Mus musculusAF071070_1 protein 856 49
kinase
Myak-L
1133 gi5815145Mus musculusAF170304_1 nuclear 856 49
body
associated kinase
2b
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TABLE 2 B
SEQ Hit_ID Species Description S scorePercentage-
ID ' Identi
1134 gi22267965Homo SapiensSimilar to KIAA14233 100
protein 22
1134 gi7243227Homo SapiensHIAA1423 protein _ 100
3
22
1134 gi7300805Drosophila CG13409-PA _ 51
melanogaster 171
1135 ' 13529338Mus musculus 1862 48
1135 gi14571502Homo Sapienscalcium-promoted 4174 99
Ras
inactivator
1135 14185294Homo SapiensrasGAP-activating-like1891 48
protein
1137 115128103Mus musculusAF397007 1 nephronectin2962 87
1137 gi15128105Mus musculusAF397008 1 nephronectin2934 85
1137 gi15430246Mus musculusnephronectin short 2802 83
isoform
1138 gi16041675Homo SapiensAAH15704 joined 2622 100
to JAZF1
1138 gi17862954Drosophila SD04959p 904 42
melanogaster
1138 gi30046920Mus musculusDllErtd530e protein1941 96
1139 gi12654929Homo SapiensAAH01311 mesenchymal719 74
stem
cell protein DSCD75
1139 gi17512251Homo SapiensAAH19104 mesenchymal716 74
stem
cell protein DSCD75
1139 gi7638247Homo SapiensAF242773_1 mesenchymal719 74
stem cell protein
DSCD75
1140 gi32967231Homo sapiensTAFA3 481 100
1140 gi32967237Homo SapiensTAFA3.2 923 100
1140 gi32967243Mus musculusTAFA3 390 82
1141 gi32967231Homo sapiensTAFA3 738 100
1141 gi32967237Homo SapiensTAFA3.2 481 100
1141 132967243Mus musculusTAFA3 634 87
1142 '10443967Homosapiens AF268610_1 THEGprotein1934 88
1142 gi20306274Homo sapienstesticular haploid 1934 88
expressed
gene
1142 gi7416134Homo Sapienstestis-specific 1934 88
gene
1143 gi21928259Homo Sapiensseven transmembrane1023 100
helix
receptor
1143 gi219284.96Homo Sapiensseven transmembrane1023 100
helix
receptor
1143 gi21928655Homo Sapiensseven transmembrane916 89
helix
receptor
1144 gi18480746Mus musculusolfactory receptor 1278 79
MOR261-10
1144 gi21928655Homo Sapiensseven transmembrane1456 93
helix
receptor
1144 gi32052225Mus musculusolfactory receptor 1278 79
GA_x6IC02T2P3E9-4341246-
4340281
1146 gi15779092Homo sapiensAAH14613 Similar 1295 100
to syntaxin
18
1146 130583139Homo Sapienssyntaxin 18 1295 100
1146 gi30585223synthetic Homo Sapiens syntaxin1295 100
construct 18
1147 gi14573319Homo SapiensAF334755_1 interleukin-1812 99
HY2
1147 gi14573321Homo SapiensAF334756_1 interleukin-1812 99
HY2
1147 gi18025344Homo Sapiensinterleukin-1 receptor809 99
anta onist-like
FILL theta
1148 gi 1668744Homo SapiensHHaS hair keratin 1114 72
type I
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TART.F 7 R
SEQ Hit Species Description S scorePercentage_
ID ID
I denti
intermediate filament
1148 gi3724107Homo sapiens type I hair keratin1114 72
5
1148 gi4103158Mus musculus hair keratin acidic1116 72
5; Ha5
keratin
1149 gi23271416Mus musculus Leprel protein 141 30
1149 gi30582917Homo Sapiens 1 139 30
1149 gi6166378Mus musculus AF165163_1 growth 143 30
suppressor 1L
1150 gi16550754Homosapiens unnamed protein 1337 90
roduct
1150 gi1699265Homo Sapiens malignant cell 389 57
expression-
enhanced gene/tumor
pro ession-enhanced
ene
1150 gi27529955Mus musculus mBB 1 1284 86
1151 gi 14595019Homo Sapiens keratin 6 irs 1990 76
1151 gi18031724Mus musculus keratin protein 1948 75
I~6irs
1151 gi27901522Homo Sapiens keratin 6 irs3 2519 94
1152 gi11066090Homo Sapiens AF195192_1 matrix 2233 84
metalloprotease
MMP-27
1152 gi12006364Tupaia belangeriAF281673_1 matrix 1859 71
metalloproteinase-27
1152 gi3511149Gallus gallusmatrix metalloproteinase1213 50
1153 gi11066090Homo Sapiens AF195192_1 matrix 2233 84
metalloprotease
MMP-27
1153 gi12006364Tupaia belangeriAF281673_I matrix 1859 71
metalloproteinase-27
1153 gi3511149Gallus gallusmatrix metalloproteinase1213 50
1154 gi24710913Homo Sapiens suppressor of fused2599 100
1154 gi5739507Homo Sapiens AF175770_1 suppressor2594 99
of
fused
1154 gi6689894Homo Sapiens AF159447_1 Suppressor2599 100
of
Fused
1155 gi20387085~ncorhynchus -1 680 31
mykiss
1155 gi21667212Homo Sapiens AF465766_I 2600 100
bactericidal/permeability-
increasing protein-like
2
1155 gi28173296Cyprinus carpiobactericidal permeability-702 31
increasing
protein/lipopolysaccharide-
binding protein
1156 gi12082687Homo Sapiens Sry-related HMG-box2066 100
protein
1156 gi24047297Homo Sapiens SRY-box 18 2066 100
1156 gi8894593Homo Sapiens S~318 protein 2066 100
1157 gi19526647Homo Sapiens AF462348_1 oxidored-nitro842 92
domain-containing
protein
1157 gi21758574Homo Sapiens unnamed protein 922 97
product
1157 gi7303522Drosophila CG13178-PA 173 32
melanogaster
1158 gi19526647Homo Sapiens AF462348_1 oxidored-nitro842 92
domain-containing
protein
1158 gi21758574Homo Sapiens unnamed protein 922 97
product
1158 gi7303522Drosophila CG13178-PA 173 32
melanogaster
1159 gi1794221Mus musculus DNA ligase III-beta2977 89
1159 gi1794223Mus musculus DNA li ase III-alpha2977 89
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TABLE 2 B
SEQ Hit_ID Species Description S Percentage_
ID I scoredenti
1159 gi29165722Mus musculus ligase III, DNA, 3010 89
ATP-
dependent
1160 gi1052871Homo Sapiens squamous cell carcinoma879 45
antigen 2
1160 gi15667919Homo Sapiens AF411191 1 SERPINB122063 95
1160 gi887465Homo sapiens leupin 879 45
1163 gi29611342Homo Sapiens AF425650_1 MBDl- 352 52
containing chromatin
associated
factor
1163 gi7228149Mus musculus ATFa-associated 357 29
factor
_ gi7303705Drosophila CG12340-PA 187 31
1163 melanogaster
1166 gi14211398Homo Sapiens AF380342_1 caspase-8L263 100
1166 gi19401527Homo Sapiens procaspase-8 223 95
1166 gi20381326Homo Sapiens Similar to caspase 263 100
8, apoptosis-
related cysteine
protease
1167 gi10440448Homo Sapiens FLJ00060 protein 1204 98
1167 gi30466084Bos taurus killer cell immunoglobulin-like800 53
receptor KIR3DS1
1167 gi30466086Bos taurus killer cell immunoglobulin-like783 53
receptor ICIR3DL1
1168 gi1799570Rattus norvegicusTIP120 4573 99
1168 gi29792160Homo Sapiens TIP120 protein 4586 99
1168 gi7688703Homo Sapiens AF157326 1 TIP120 4573 99
protein
1169 gi13016701Homo Sapiens activating coreceptor1226 100
NI~p80
1169 gi22449867Maraca fascicularisNI~p80 NK receptor 1122 90
1169 gi7188567Homo Sapiens AF175206_1 lectin-like1226 100
receptor F1
1171 gi21619190Homo sapiens -like 1X-linked 2785 100
1171 gi3021409Homo Sapiens like 1 protein 3057 100
1171 gi30353941Homo Sapiens TBL1X protein 3057 100
1172 gi1699265Homo sapiens malignant cell expression-671 65
onhane~d gene/tumor
progression-enhanced
gene
1172 gi27529955Mus musculus mBB 1 646 67
1172 gi33355691Homo Sapiens transmembrane channel-like642 100
protein 4
1173 gi1699265Homo Sapiens malignant cell expression-671 65
enhanced gene/tumor
progression-enhanced
gene
1173 127529955Mus musculus mBBl 646 67
1173 gi33355691Homo Sapiens transmembrane channel-like642 100
protein 4
1174 gi16550754Homo Sapiens unnamed protein 1881 100
product
1174 gi1699265Homo sapiens malignant cell expression-930 81
enhanced geneltumor
pro ession-enhanced
ene
1174 gi27529955Mus musculus mBB 1 1810 95
1175 gi13182755Homo Sapiens AF212237 1 HPHRP 1210 100
1175 gi15929309Homo Sapiens Phosphotriesterase 1210 100
related
1175 gi29791939Homo Sapiens phosphotriesterase 1210 100
related
1177 gi10047271Homo sapiens KIAA1598 protein 789 99
1177 gi22539701Mus musculus 4930506M07Rik protein818 96
1177 gi26349641Mus musculus unnamed protein 818 96
product
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TABLE 2 B
SEQ_IDHit Species Description S_scorePercentage_
ID I denti
1178 gi14272704Homo Sapiens unnamed protein 157 96
product
1178 gi19575509Homo sapiens unnamed protein 164 100
product
1178 gi19575655Homo Sapiens unnamed protein 164 100
product
1182 gi13377880Cricetulus AF336043_1 arginine3253 85
lon icaudatusN-
methyltransferase
p82 isoform
1182 gi13377882Cricetulus AF336044_1 arginine3253 85
longicaudatusN-
methyltransferase
p77 isoform
1182 '13879453Mus musculus cDNA sequence BC0067053260 85
1183 gi14424574Homo Sapiens AAH09315 phosphatidylserine777 100
decarboxylase
1183 gi16306618Homo Sapiens AAH01482 phosphatidylserine1218 96
decarboxylase
1183 gi191185Cricetulus phosphatidylserine 1128 88
griseus decarboxylase
1184 gi10086253Homo Sapiens glucocorticoid-induced460 98
GILZ
1184 gi11907580Mus musculus AF201289_1 TSC22-related891 87
inducible leucine
zipper 3c
1184 gi5919161Homo Sapiens AF183393_1 TSC-22-like460 98
Protein
1185 113874437Homo Sapiens cerebral protein-111457 68
1185 120987344Mus musculus LOC212904 protein 3064 89
1185 gi24980850Homo Sapiens 3283 100
1186 gi14~035978Homo Sapiens unnamed protein 2577 100
product
1186 gi14~272784Homo Sapiens unnamed protein 2577 100
product
1186 gi16923351Homo sapiens AF204270_1 RbBP-35 1431 99
1187 gi18676660Homo Sapiens FLJ00229 protein 930 97
1187 gi19343701Mus musculus RIKEN cDNA A630054L15913 93
1187 gi25955706Homo Sapiens Similar to hypothetical936 97
protein
MGC38041
1188 gi17865311Homo Sapiens AF452102 1 dipeptidyl4646 100
peptidase-like protein
9
1188 gi2754~9552Homo Sapiens dipeptidyl peptidase4646 100
IV-related
protein-2
1188 129293087Homo Sapiens dipeptidyl peptidase4787 99
9
1189 gi17865311Homo Sapiens AF452102 1 dipeptidyl4384 95
peptidase-like protein
9
1189 gi27549552Homo Sapiens dipeptidyl peptidase4384 95
IV-related
protein-2
1189 gi29293087Homo Sapiens dipeptidyl peptidase4525 95
9
1190 gi17865311Homo Sapiens AF452102 1 dipeptidyl4551 98
peptidase-like protein
9
1190 gi27549552Homo Sapiens dipeptidyl peptidase4551 98
IV-related
protein-2
1190 gi29293087Homo Sapiens dipeptidyl peptidase4692 98
9
1191 113097642Homo Sapiens Ribosomal protein 554 99
S25
1191 113279149Homo Sapiens Ribosomal protein 554 99
S25
1191 gi13436422Homo Sapiens Ribosomal protein 554 99
S25
1192 gi16549206Homo Sapiens unnamed protein 680 100
product
1193 gi21756739Homo Sapiens unnamed protein 4771 97
product
1193 gi6453538Homo Sapiens hypothetical protein4159 99
1193 gi6634025Homo Sapiens KIAA0379 protein 3467 67
1194 gi12652695Homo Sapiens AAH00096 HtrA-like 2116 93
serine
protease
1194 gi5870865Homo Sapiens serine protease 2116 93
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TABLE 2 B
SEQ Hit Species Description S Percentage_
ID ID I scoredenti
1194 gi7672669Homo Sapiens AF141305_1 serine 2116 93
protease
Htra2
1195 gi1387985Homo Sapiens A3 adenosine receptor904 100
1195 120988265Homo Sapiens adenosine A3 receptor904 100
1195 gi22658481Homo Sapiens adenosine receptor 904 100
A3
1196 gi24078514Mus musculus AF454954 1 crossveinless-2988 91
1196 gi32816043Mus musculus BMP-binding endothelial988 91
regulator precursor
protein
1196 gi32892146Homo Sapiens crossveinless-2 1085 100
1197 gi18479346Mus musculus olfactory receptor 1334 82
MOR101-1
1197 gi 18480772Mus musculus olfactory receptor 1415 84
MOR101-2
1197 gi32054443Mus musculus olfactory receptor 1415 84
GA_x6K02T2PBJ9-2443810-
2444775
1198 gi16502169Salmonella putative DNA methylase751 93
enterica
subsp. enterica
serovar Typhi
1198 gi29137981Salmonella putative DNA methylase751 93
enterica
subsp. enterica
serovar Typhi
Ty2
1198 gi498768Serratia marcescensDeoxyadenosyl- 330 51
methyltransferase
1199 gi1213589Xenopus laevisProsta landin D 290 33
Synthase
1199 gi16974751Gallus gallusCALM 335 37
1199 gi666121~enopus laeviscpl-1 291 33
1200 gi20987993Mus musculus MGC41336 protein 1212 90
1200 gi22296200Thermosynechococcasparaginyl-tRNA 1046 46
us elongatus synthetase
BP-1
1200 gi32448516Pirellula asparaginyl-tRNA 1034 47
sp. synthetase
1201 gi20067381Homo Sapiens ALMS1 protein 242 41
1201 gi21552774Mus musculus AF425257_1 Almstrom217 38
syndrome 1 protein
1201 gi32693320Homo sapiens ALMS 1 protein 242 41
1202 gi12655061Homo Sapiens AAH01380 495 92
1202 gi23574788Maraca fascicularissuccinate dehydrogenase502 93
flavoprotein subunit
1202 gi5759173Homo Sapiens succinate dehydrogenase495 92
flavoprotein subunit
1203 gi21928186Mus musculus GPI-gamma 4; GPIgamma41466 61
1203 gi21928188Mus musculus GPI- amma 4; GPI 1466 61
amma4
1203 gi30931171Mus musculus GPI amma4 protein 1466 61
1204 gi15082311Homo Sapiens AAH12061 -binding 1534 92
protein 3
1204. gi9957161Mus musculus AF176327_l alphaCP-31708 99
1204 gi9957165Homo Sapiens AF176329_1 alphaCP-31722 100
1205 gi 14574118CaenorhabditisDumpy : shorter 233 31
ele ans than wild-type
protein 19
1205 gi16553246Homo Sapiens unnamed protein 881 99
product
1205 gi21739662Homo Sapiens hypothetical protein830 95
1206 112653341Homo Sapiens AAH00439 beta 1742 94
1206 gi12804943Homo Sapiens AAH01924 beta 1742 94
1206 gi31071Homo Sapiens E-1 beta subunit 1742 94
of the
pyruvate dehydrogenase
complex
1207 gi164851Oryctolagus calsequestrinprecursor1908 94
~ ~
CA 02500521 2005-03-30
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235
TABLE 2 B
SEQ Hit Species Description S Percentage_
ID ID I scoredenti
cuniculus
1207 '2618621Mus musculus skeletal muscle 1938 94
calsequestrin
1207 gi688292Homo Sapiens calmitine; calsequestrine2029 100
1209 gi10432376Homo Sapiens 3334 99
1209 111034760Homo Sapiens NIBAN 3692 99
1209 '12620192Homo Sapiens AF288391 1 Clorf24 4775 99
1210 gi2982508Homo Sapiens TCR beta chain 1290 93
1210 gi3002925Homo Sapiens T cell receptor 1277 93
beta chain
1210 gi3089433Homo Sapiens T cell receptor 1028 75
beta chain
1211 gi12006041Homo Sapiens AF267857_1 AD038 761 98
1211 gi14189960Homo Sapiens AF305818_1 PR00764 141 53
1211 gi33338042Homo Sapiens AF173896_1 MSTP121 143 46
1213 gi17939498Homo Sapiens AAH19299 protocadherin4777 99
gamma subfamily
C, 3
1213 gi20072790Homo sapiens protocadherin gamma4777 99
subfamily C, 3
1213 gi2995719Homo sapiens protocadherin 43 4792 100
1214 gi12803363Homo sapiens CALR protein 1747 99
1214 gi18088117Homo Sapiens AAH20493 calreticulin1747 99
1214 gi30583735Homo sapiens calreticulin 1747 99
1215 gi200962Mus musculus serine 1 ultra high254 38
sulfur
protein
1215 gi200964Mus musculus serine 2 ultra high299 43 '
sulfur
protein
1215 gi3228237Homo sapiens ultra hi h sulfer 248 36
keratin
1218 gi17223709Homo Sapiens selenoprotein SeIM 235 100
1218 gi17223711Mus musculus selenoprotein SeIM 188 78
1218 gi26351995Mus musculus unnamed protein 162 76
product
1221 gi1001963Homo Sapiens osteopontin 1400 90
1221 gi189151Homo Sapiens nephropontin precursor1400 90
1221 gi992950Homo Sapiens OPN-c 1426 98
1222 gi14326586Homo Sapiens AF386078 1 serine-cysteine2252 95
proteinase inhibitor
Glade C
member 1
1222 1179130Homo Sapiens antithrombin III 2252 95
1222 gi583741synthetic Antithrombin III 2252 95
construct
1223 gi18088363Homo Sapiens AAH20669 advanced 2004 99
glycosylation end
product-
specific receptor
1223 gi1841550Homo Sapiens AAB47491 receptor 2004 99
for
advanced glycosylation
end
products
1223 gi561659Homo Sapiens receptor of advanced2004 99
glycosylation end
products of
proteins
1224 gi13359193Homo Sapiens KIAA1660 protein 598 100
1225 gi37231Homo Sapiens DNA topoisomerase 8061 99
II
1225 gi3869382Homo Sapiens DNA topoisomerase 8048 99
II beta
1225 gi790988Cricetulus 7886 97
longicaudatus
1226 gi1881713Rattus norvegicusfatty acid transport3039 87
protein
1226 '20810561Mus musculus , member 1 3031 87
1226 gi563829Mus musculus fatty acid transport3031 87
protein
1227 gi15080010Homo Sapiens AAH11789 Similar 503 44
to COPS
CA 02500521 2005-03-30
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236
TABLE 2 B
SEQ Hit Species Description S Percentage-
ID ID score
Identi
complex subunit
7a
1227 gi15215085Mus musculus Cops7b protein 885 71
1227 gi3309176Mus musculus COP9 complex subunit888 71
7b
1228 gi180251Homo Sapiens precerebellin 544 58
1228 16942096Mus musculus CBLN3 938 93
1228 16942098Mus musculus AF218380 1 CBLN3 938 93
1229 gi15620819Homo Sapiens I~IAA1880 protein 2851 99
1229 gi17861952Drosophila LD01947p 1382 50
melanogaster
1229 gi7291183Drosophila CG1826-PA 1382 50
melanogaster
1230 gi21756739Homo Sapiens unnamed protein 2878 58
product
1230 gi26354957Mus musculus unnamed protein 5453 95
product
1230 gi6634025Homo sapiens HIAA0379 protein 3166 57
1231 gi20387085Oncorhynchus -1 662 31
mykiss
1231 gi21667212Homo Sapiens AF465766_1 2384 98
bactericidal/permeability-
increasing protein-like
2
1231 gi28173296Cyprinus carpiobactericidal permeability-680 31
increasing
protein/lipopolysaccharide-
binding protein
1232 gi20387085Oncorhynchus -1 654 31
mykiss
1232 gi21667212Homo sapiens AF465766_1 2389 99
bactericidal/permeability-
increasing protein-like
2
1232 gi28173296Cyprinus carpiobactericidal permeability-672 30
increasing
protein/lipopolysaccharide-
binding protein
1233 gi20387085Oncorhynchus -1 688 31
mykiss
1233 gi21667212Homo Sapiens AF465766_1 2595 99
bactericidal/permeability-
increasing protein-like
2
1233 gi28173296Cyprinus carpiobactericidal permeability-710 31
increasing
protein/lipopolysaccharide-
binding protein
1234 gi18257341Mus musculus Expressed sequence 2106 69
AW060207
1234 gi2191168Arabidopsis contains similarity207 26
thaliana to myosin
hea chain
1234 gi2879804SchizosaccharomyceSPAC23A1.16c 163 28
s pombe
1235 gi11493528Homo Sapiens AF130117 71 PR01953671 100
1236 gi21754036Homo Sapiens unnamed protein 998 99
product
1236 gi30411057Mus musculus RIKEN cDNA B230219D22954 93
1236 131565787Homo Sapiens FLJ37562 protein 1002 100
1237 gi27469556Homo Sapiens Putative neuronal 3516 99
cell adhesion
molecule
1237 gi3068592Mus musculus punc 2976 86
1237 '4206390Homo Sapiens putative neuronal 1569 98
cell adhesion
CA 02500521 2005-03-30
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237
TABLE 2 B
SEQ Hit_ID Species Description S_scorePercentage_
ID I denti
molecule
1238 gi12667401Homo SapiensAF326731_l NUF2R 2347 99
1238 gi14317902Homo Sapienskinetochore protein2347 99
Nuf2
1238 gi18043223Mus musculusNUF2R protein 1754 73
1239 gi10435493Homo Sapiensunnamed protein 2702 99
product
1239 gi7022901Homo Sapiensunnamed protein 3682 99
product
1239 gi7688176Homo Sapienshypothetical protein3688 99
1240 gi21634823Homo SapiensAF389428_1 semaphorin5142 91
6D
isoform 3
1240 gi21634825Homo SapiensAF389429_1 semaphorin5667 98
6D
isoform 4
1240 gi21634827Homo SapiensAF389430_1 semaphorin3112 63
6D
isoform 1
1241 gi14036200Homo Sapiensunnamed protein 245 97
product
1243 gi21671105Homo SapiensRAD52B 1134 100
1243 gi23468352Homo SapiensSimilar to RAD52B 963 99
1243 gi32967621Mus musculus2410008M22Rik protein828 74
1244 gi15928404Mus musculusFasting-inducible 185 36
integral
membrane protein
TM6P1
1244 gi18490578Mus musculusA630041N19 protein 449 71
1244 gi20379926Mus musculusFasting-inducible 185 36
integral
membrane protein
TM6P 1
1245 118490578Mus musculusA630041N19 protein 875 70
1245 gi29792229Homo sapiensFLJ90024 protein _ 33
____
297
1245 gi6013381Rattus norvegicusAF186469_1 TM6P1 296 33
1246 gi28626251Homo Sapienscalcium-permeable 1194 100
store-
operated channel
TRPM3c
1246 gi28626253Homo Sapienscalcium-permeable 1194 100
store-
operated channel
TRPM3d
1246 gi28626255Homo Sapienscalcium-permeable 1194 100
store-
operated channel
TRPM3e
1247 gi17386053Mus musculusAF444274_1 Jedi 2269 50
protein
1247 gi 18044=366Homo SapiensAAH20198 Similar 3468 99
to
MEGF10 protein
1247 gi18252658Mus musculusAF461685 1 Jedi-7362269 50
protein
1248 120987880Musmusculus E130103I17Rikprotein3580 87
1248 gi28204917Mus musculusE130103I17Rik protein3801 86
1248 gi4588087Homo sapiensAF095771-1 PTH-responsive4080 94
osteosarcoma B 1
protein
1249 gi13591434Homo Sapiens 1160 100
1249 gi13591435Homo sapiens 976 99
1249 gi19913471Homo Sapiens 1265 99
1250 gi16605581Homo SapiensH-rev107-like protein_ 100
5 1451
1250 gi21707989Homo SapiensSimilar to H-rev107-like1382 96
protein 5
1250 gi6048565Homo SapiensAF092922_1 retinoid376 54
inducible
gene 1
1251 gi21263094Rattus norveAF512430 1 tramdorin1665 81
icus 1
1251 127924388Mus musculusTramdorin 1 1668 82
1251 gi31871293Homo Sapiensprotonlamino acid 2010 99
transporter 2
1252 gi14571904Rattus norvegicusAF361239_1 lysosomal1931 78
amino
acid transporter
1
1252 gi31324239Homo Sapiensproton-coupled amino2174 90
acid
transporter
CA 02500521 2005-03-30
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238
TABLE 2 B
SEQ Hit ID Species Description S Percentage_
ID score
I denti
1252 '31871291Homo Sapiens_ 2195 90
proton/amino acid
transporter 1
1254 gi1563885Homo Sapiensfibroblast growth 917 90
factor
homologous factor
1
1254 gi1669500Mus musculusfibroblast growth 917 90
factor
homologous factor
1
1254 gi20988932Mus musculusFgfl2 protein 916 98
1255 gi19263005Ciona intestinalisleucine-rich repeat759 75
dynein light
chain
1255 gi2760161Anthocidarisouter arm dynein 658 67
light chain 2
crassispina
1255 gi7303901Drosophila CG8800-PA 554 58
melanogaster
1256 gi12666529Mus musculusb,b-carotene-9',10'-2356 80
dioxygenase
1256 gi12666531Homo Sapiensputative b,b-carotene-9',10'-2982 99
dioxygenase
1256 gi14582265Homo SapiensAF276432_1 putative2918 99
carotene
dioxygenase
1257 gi12666529Mus musculusb,b-carotene-9',10'-2305 81
dioxygenase
1257 gi12666531Homo Sapiensputative b,b-carotene-9',10'-2850 96
dioxygenase
1257 gi14582265Homo SapiensAF276432_1 putative2786 95
carotene
dioxygenase
1258 gi15559697Homo SapiensAAH14205 Similar 157 28
to neural
cell adhesion molecule
1
1258 gi28703938Homo SapiensSimilar to neural 157 28
cell adhesion
molecule 1
1258 gi61 Bos taurus calmodulin-independent158 28
adenylate cyclase
1260 gi1079734Mus musculuscitron 1291 94
1260 gi2745840Rattus norvegicuspostsynaptic density1262 93
protein;
citron
1260 gi3599509Mus musculusrho/rac-interacting1286 94
citron
lcinase
1261 gi28277755Danio rerio proteinase inhibitor,479 30
Glade E,
member 2
1261 gi28435507Sus scrofa nexin-1 467 30
1261 gi32485107Homo Sapiensnexin-related serine2002 92
protease
inhibitor
1262 113383364Homo Sapiensclaudin-1 223 97
1262 gi15214678Homo SapiensAAH12471 claudin 223 97
1
1262 gi7381083Homo SapiensAF134160 1 claudin-1223 97
1263 gi13542685Mus musculusSARla gene homolog 441 54
1263 gi21634445Homo SapiensAF274026_1 GTP-binding446 57
protein Sara
1263 gi33150636Homo sapiensAF087897_1 GTP binding446 57
protein
1264 gi22902436Mus musculusSphingosine-1-phosphate717 38
phosphatase 1
1264 gi23345324Homo Sapienssphingosine 1-phosphate2073 100
phosphohydrolase
2
1264 gi29436890Mus musculusSimilar to sphingosine-1-1624 80
phosphate phosphotase
2
1265 gil4 Bos taurus BoWCl.l 1214 39
CA 02500521 2005-03-30
WO 2004/080148 PCT/US2003/030720
239
TABLE 2 B
SEQ Hit_ID Species Description S scorePercentage_
ID I denti
1265 gi1480365Sus scrofa scavenger-receptor 1327 42
protein
1265 gi27464818Mus musculusscavengerreceptor 1339 44
cysteine-
rich type 1 protein
CD163c-
alpha precursor
1266 gil4 Bos taurus BoWCl.l 1214 39
1266 gi1480365Sus scrofa scavenger-receptor 1327 42
protein
1266 gi27464818Mus musculusscavengerreceptorcysteine-1339 44
rich type 1 protein
CD163c-
alpha precursor
1268 gi21619491Homo Sapienssimilar to expressed778 100
sequence
AW049604
1268 gi32967233Homo SapiensTAFA4 778 100
1268 gi32967245Mus musculusTAFA4 698 93
1270 gi18033185Danio rerio AF330001_1 LJNC45-related3100 73
protein
1270 gi27436424Mus musculusstriated muscle 3937 94
UNC45
1270 gi27436426Homo Sapiensstriated muscle 4092 99
1JNC45
1271 gi21064657Drosophila RH01479p 182 39
melano aster
1271 gi28375475Homo Sapiensunnamed protein 639 99
product
1271 gi7304173Drosophila CG1577-PA 182 39
melano aster
1272 gi16876958Homo SapiensAAH16754 hypothetical410 100
protein MGC12217
1273 gi15823642Homo sapiensALS2CR7 2038 100
1273 gi32485022Homo Sapiensserine/threonine 2038 100
protein kinase
1273 gi32485027Homo Sapiensserine/threonine 2320 100
protein kinase
1274 gi12654893Homo SapiensAAH01291 400 97
1274 gi2407911Homo Sapiens0016 714 96
1274 gi6733554unidentifiedunnamed protein 710 96
product
1275 gi18147612Homo Sapiensmetalloprotease 4434 95
disintegrin
1275 gi21908028Homo SapiensAF466287_1 a disintegrin4434 95
and
mctalloproteasc
doanain 33
1275 gi21908030Homo Sapiensa disintegrin and 4434 95
metalloprotease
domain 33
1276 gi16551401Homo Sapiensunnamed protein 2735 100
product
1276 gi4972116Arabidopsis putative proline-rich133 44
thaliana protein
1276 gi7269638Arabidopsis putative proline-rich133 44
thaliana protein
1277 gi15291913Drosophila LD31582p 204 23
melanogaster
1277 gi22477165Homo sapiens 2783 100
1277 gi26326895Mus musculusunnamed protein 1752 69
product
1278 gi3452275Pseudopleuronectesaminopeptidase N 1008 37
americanus
1278 gi525287Susscrofa aminopeptidase N. 1014 38
1278 gi544755Oryctolagus aminopeptidase N; 1021 37
cuniculus APN
1279 gi13559063Homo Sapiens 747 100
1279 gi24416538Mus musculus1700001D09Rik protein708 71
1279 gi9963863Homo SapiensAF226731_1 AD026 738 98
1281 gi20810533Homo Sapienshypothetical gene 414 100
supported by
AK054745; AK054745;
AK054745; AK054745
1282 gi20810533Homo Sapienshypothetical gene 795 100
~ ~ supported by
CA 02500521 2005-03-30
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240
TABLE 2 B
SEQ Hit ID Species Description S scorePercentage_
ID I denti
AK054745; AK054745;
AK054745; AK054745
1282 gi26345254Mus musculusunnamed protein 367 63
product
1282 '33244011Mus musculus 374 64
1283 gi20810533Homo Sapienshypothetical gene 789 99
supported by
AK054745; AK054745;
AK054745; AK054745
1283 126345254Mus musculusunnamed protein 396 64
product
1283 gi33244011Mus musculus 403 65
1284 gi18447388Drosophila RE05944p 700 31
melanogaster
1284 gi21645210Drosophila CG30394-PA 700 31
melanogaster
1284 gi21645211Drosophila CG30394-PB 700 31
melano aster
1285 gi14035874Homo Sapiensunnamed protein 910 99
product
1285 gi14035876Homo Sapiensunnamed protein 853 99
product
1285 gi20070842Homo Sapienssimilar to hypothetical997 99
protein
FLJ13448
1286 gi19070822Mus musculusAF364868_1 Myb protein145 23
P42POP
1286 gi20977688~ienopus tumorhead 146 33
laevis
1286 gi27881626Homo SapiensL~C339344 protein 150 25
1287 ' 10433236Homo Sapiensunnamed protein 721 99
product
1288 gi13278415Mus musculuscDNA sequence BC0040182402 98
1288 126355239Mus musculusunnamed protein 2256 97
product
1288 gi30354720Mus musculuSAI427653 protein 1357 57
1289 gi12698037Homo SapiensKIAA1746 protein 5541 100
1289 gi16769274Drosophila LD22423p 210 24
melanogaster
1289 gi7298509Drosophila CG18398-PA 214 24
melanogaster
1290 gi21391484Homo Sapiensleucine-rich repeat397 39
domain-
containing protein
1290 gi21391486Mus musculusleucine-rich repeat433 4~0
domain-
containing protein
1290 gi21623740Rattus norvegicusLeucine-rich repeat-containing428 40
protein 3
1291 gi20269073Homo Sapiensputative lipid kinase2006 76
1291 121624340Homo Sapiensceramide kinase 2006 76
1291 gi21624342Mus musculusceramide kinases 1617 64
1292 gi312590Mus musculusbiliary glycoprotein193 32
1292 gi3549152Homo SapiensR29124_1 175 31
1292 gi7414626Rattus norvegicuscarcinoembryonic 176 31
antigen-
related cell adhesion
molecule,
secreted isoform
CEACAMla-
4C1
1293 11197500Homo SapiensT-cell surface anti182 22
en
1293 121707370Homo Sapiens, sheep red blood 182 22
cell receptor
1293 gi312590Mus musculusbiliary glycoprotein193 32
1294 gi18676564Homo SapiensFLJ00179 protein 993 99
1294 gi21411450Mus musculusC230093N12Rilc protein1159 91
1294 gi28839684Homo SapiensSimilar to expressed1242 99
sequence
AI426465
DEMANDE OU BREVET VOLUMINEUX
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