Note: Descriptions are shown in the official language in which they were submitted.
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DIAGNOSING IDH1 RELATED SUBGROUPS AND TREATMENT OF CANCER
STATEMENT REGARDING FEDERALLY-SPONSORED RESEARCH
This invention was made with government support under Grant No. NS064952-01A1
awarded by the National Institute of Health. The government has certain rights
in the invention.
FIELD OF THE INVENTION
The invention relates to medicine, for example, methods, compositions and kits
for
classifying and treating tumors.
BACKGROUND
All publications cited herein are incorporated by reference in their entirety
to the same
extent as if each individual publication or patent application was
specifically and individually
indicated to be incorporated by reference. The following description includes
information that
may be useful in understanding the present invention. It is not an admission
that any of the
information provided herein is prior art or relevant to the presently claimed
invention, or that any
publication specifically or implicitly referenced is prior art.
WHO grade IV astrocytoma or glioblastoma (GBM) are the most common primary
brain
tumors and, unfortunately, the most aggressive. Median survival of patients
harboring these
tumors is approximately 14 months. Despite a committed effort to investigate
new
chemotherapies, molecularly targeted therapies, immunotherapies, surgical and
radiological
approaches, there has been little improvement over the last 30 years.
Inadequate classification of
GBM may have contributed to the difficulty of developing new therapies by
decreasing power of
clinical trials and underestimating benefit of class-specific drugs. It may
also have confounded
discovery of class-specific pathways and drug targets.
GBM diagnosed by histopathology is a collection of molecular and clinical
subtypes. For
example, there are two classes of GBM based on clinical presentation [1], [2].
Primary GBM
arise de novo in older patients and are associated with poorer prognosis.
Secondary GBM are
rare (-5-10% of total GBM), progress from lower grade tumors, occur more
frequently in
younger patients with better prognosis and have a different molecular profile.
Studies using gene
expression, DNA copy number, miRNA, and DNA methylation show these molecular
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characteristics can divide GBM into subclasses, some with different clinical
characteristics [3],
[4], [5], [6], [7], [8], [9]. Three subtypes emerged in early studies of WHO
grade IV GBM
(studies that combine histological subtypes or grades of glioma and use
molecular classification
to distinguish them are excluded from this discussion). These were called
proneural (PN),
Proliferative (PROLIF) and mesenchymal (MES) and each had characteristic
clinical and
molecular features [4]. Later approaches find 3-5 GBM subtypes including the
PN, MES and
Classical (CLAS) subgroups [8], [9], [10], [11]. DNA methylation identifies a
subset of PN
tumors with glioma CpG island methylator phenotype (GCIMP) that are younger,
longer
surviving and tightly associated with IDH1 mutations [8].
However, molecular classification of GBM is still in its infancy. There is no
consensus on
the number of subtypes and which classifiers should be used to classify them.
In addition, there
is considerable reassignment of tumors to different classes depending on
classifier used. There is
also little information on which oncogenic pathways are active in subtypes and
how subtypes
respond to standard and experimental therapeutics.
Alterations in the growth factor receptor/phosphatidylinositol 3-kinase/AKT
(GFR/PI3K/AKT) pathway occur in most human cancers including at least 85% of
GBM [10].
Pharmacological inhibition of the GFR/PI3K/AKT pathway is a promising strategy
for anti-
cancer therapy [12], [13]. However, while sporadic responses have been
reported, clinical trials
of pathway inhibitors in GBM have been largely disappointing [14].
SUMMARY OF THE INVENTION
Various embodiments of the present invention provide a method for classifying
a cancer
in a subject. The method may consist of or may consist essentially of or may
comprise:
obtaining a biological sample from the subject; determining an expression
pattern of AKT
pathway components in the biological sample; and classifying the cancer based
on the
determined expression pattern of AKT pathway components in the biological
sample.
Various embodiments of the present invention provide a method for diagnosing
whether a
subject has a cancer subtype. The method may consist of or may consist
essentially of or may
comprise: obtaining a biological sample from the subject; determining whether
an expression
pattern of AKT pathway components is present in the biological sample; and
diagnosing the
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subject as having the cancer subtype if the expression pattern of AKT pathway
components is
determined to be present in the biological sample. In various further
embodiments, the method
comprises selecting, choosing or prescribing a therapeutic for the subject
after diagnosis. In
various further embodiments, the method comprises instructing or directing the
subject to receive
a therapeutic after diagnosis. In various further embodiments, the method
comprises
administering a therapeutically effective amount of a therapeutic to the
subject, thereby treating,
preventing, reducing the likelihood of having, reducing the severity of and/or
slowing the
progression of the diagnosed cancer subtype. In some embodiments, the cancer
subtype is an
AKT subtype including but not limited to Cl, PN, MES, CLAS, SL, and PROLIF
subtypes.
Various embodiments of the present invention provide a method for treating,
preventing,
reducing the likelihood of having, reducing the severity of and/or slowing the
progression of a
cancer subtype in a subject. The method may consist of or may consist
essentially of or may
comprise: obtaining a biological sample from the subject; determining whether
an expression
pattern of AKT pathway components is present in the biological sample;
providing a therapeutic;
and administering a therapeutically effective amount of the therapeutic to the
subject if the
expression pattern of AKT pathway components is determined to be present in
the biological
sample, thereby treating, preventing, reducing the likelihood of having,
reducing the severity of
and/or slowing the progression of the cancer subtype. In some embodiments, the
cancer subtype
is an AKT subtype including but not limited to Cl, PN, MES, CLAS, SL, and
PROLIF subtypes.
Various embodiments of the present invention provide a method for treating an
AKT
cancer subtype in a subject. The method may consist of or may consist
essentially of or may
comprise: providing a therapeutic; and administering a therapeutically
effective amount of the
therapeutic to the subject, thereby treating the AKT cancer subtype in the
subject.
Various embodiments of the present invention provide a kit for classifying a
cancer in a
subject and/or for diagnosing whether a subject has a cancer subtype. The kit
may consist of or
may consist essentially of or may comprise: one or more detection agents that
specifically bind
to one or more AKT pathway components; instructions for using the one or more
detection
agents to classify the cancer in the subject, and/or diagnose whether a
subject has the cancer
subtype.
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Various embodiments of the present invention provide a kit for treating,
preventing,
reducing the likelihood of having, reducing the severity of and/or slowing the
progression of a
cancer subtype in a subject. The kit may consist of or may consist essentially
of or may
comprise: one or more detection agents that specifically bind to one or more
AKT pathway
components; a quantity of a therapeutic; and instructions for using the one or
more detection
agents and the therapeutic to treat, prevent, reduce the likelihood of having,
reduce the severity
of and/or slow the progression of the cancer subtype in the subject
Various embodiments of the present invention provide a kit for treating an AKT
cancer
subtype in a subject. The kit may consist of or may consist essentially of or
may comprise: a
quantity of a therapeutic; and instructions for using the therapeutic to treat
the AKT cancer
subtype in the subject.
Various methods, compositions, and kits of the present invention find utility
in the
classification and treatment of various tumors, including but not limited to
various forms of brain
tumors.
BRIEF DESCRIPTION OF THE DRAWINGS
Exemplary embodiments are illustrated in referenced figures. It is intended
that the
embodiments and figures disclosed herein are to be considered illustrative
rather than restrictive.
Figure 1 depicts, in accordance with various embodiments of the invention,
that AKT
pathway gene expression classifies GBM. (A) Consensus heat maps for k = 5 to 8
generated
with AKT pathway genes in the discovery dataset (GBM195). Red indicates total
consensus
(consensus index of 1) while white indicates no consensus (consensus index of
0). (B) Silhouette
scores for k = 5 to 8 were calculated as described [26]. Samples with negative
silhouette scores
were removed in all further analysis. (C) Consensus CDF for k = 2 to 10. (D)
Effect of k on
survival differences between subgroups. Kaplan Meier curves of patient
subgroups were
generated for k = 2 to 10. For each k, Bonferroni corrected log rank p values
were generated by
pairwise comparison of subtypes. The smallest pairwise p value for each k is
plotted.
Figure 2 depicts, in accordance with various embodiments of the invention,
validation of
AKT subgroups in an independent dataset. AKT pathway genes in discovery (A)
and validation
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(B) datasets have similar patterns of expression in subgroups. Tumors in the
discovery and
validation set were first grouped by AKT subgroup membership then ordered by
correlation
coefficient. AKT gene order in the discovery set was determined by one-way
hierarchical
clustering and retained in the validation set. Discovery (C) and validation
(D) datasets have
similar DNA CNA. The percentage of patients in the discovery (A) and
validation (B) datasets
with copy number gains or losses in chr7, 10 and 19q is shown.
Figure 3 depicts, in accordance with various embodiments of the invention, Akt
classification for 5 glioblastoma subgroups. Previous classification systems
distribute non-
randomly in AKT subgroups. Distribution of Phillips (A), TCGA (B) and G-CIMP
(C)
subgroups in AKT subgroups.
Figure 4 depicts, in accordance with various embodiments of the invention,
that AKT
subgroups are prognostic. Kaplan Meier survival curves plotted for Phillips
(A) and AKT (B)
subgroups in the discovery dataset and for TCGA (C) and AKT (D) subgroups in
the validation
dataset. Log rank p value = 0.0005 (B; SL vs. rest); 0.0029 (B; PROLIF vs.
rest) and 0.003 (D;
SL vs rest). Survival differences did not reach significance in (A) and (C).
Figure 5 depicts, in accordance with various embodiments of the invention,
evidence that
SL subtype (AKT subgroup 5) patients are sensitive to alkylating agents BCNU
and CCNU.
Kaplan Meier survival curves for TCGA patients receiving (solid line) or not
receiving (dashed
line) alkylating agent (BCNU and/or CCNU) by subgroup. p = 0.03 after
correcting for age (SL
subtype; log rank). n = 6 and 16 for SL patients receiving or not receiving
BCNU/CCNU,
respectively.
Figure 6 depicts, in accordance with various embodiments of the invention,
that AKT
subgroups have distinct genomic alterations. (A) Copy number alterations in
TCGA AKT
subgroups. The GISTIC method was applied to TCGA samples in each subgroup with
copy
number information. Data are presented as a G score which is an integrated
score of the
prevalence of the copy-number change times the average (log2-transformed)
amplitude. The
green line shows significance threshold (FDR q values to account for multiple-
hypothesis
testing). Regions with subgroup-specific CNA are highlighted in yellow. (B)
Distribution of
clinical information and mutations, CNA and mRNA expression for glioma-
associated genes in
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AKT subgroups. The 218 TCGA GBM cases with gene expression, consensus putative
copy
number alteration and validated mutation data [55], [56] was used for this
analysis (The cBio
Cancer Genomics Portal; http://www.cbioportal.org/). Gene expression is
represented as z scores
calculated relative to diploid tumors for each gene and are the median value
of 3 mRNA
platforms (Affymetrix U133A and Exon arrays and Agilent custom array). There
was a
statistically significant enrichment of IDH1 mutations in the SL and EGFR and
CDKN2A
mutations plus CNA in the CLAS subtype (p < 0.02).
Figure 7 depicts, in accordance with various embodiments of the invention,
that
subgroups have distinct patterns of expression for PI3K/AKT/mTOR pathway
components
(distinct Akt pathway activation). Tumors (x axis) were grouped by AKT class
then Z
transformed mRNA (A) or protein and phospho-protein expression (B) color coded
to reflect
magnitude (y axis). The Pearson correlation coefficient for AKT pS473 vs. RPS6
pS235/236
(light gray) and AKT pS473 vs. RPS6 pS240/244 (dark gray) for each subgroup is
shown (C).
Proposed AKT/mTOR/S6 pathway map for the MES and SL subtypes based on this
data (D).
This model shows loss of AKT and mTOR inhibitors (PHLPP, TSC and pAMPK)
increases
output of the AKT/mTOR/S6 axis (pRPS6) in the MES subgroup. Conversely,
increased
expression of these inhibitors decreases output in the SL subgroup. Red, grey
and green represent
high, intermediate and low expression/activity, respectively. Dashed line is
indirect interaction.
Figure 8 depicts, in accordance with various embodiments of the invention,
summary of
features in AKT subtypes (AKT Cl/subgroup 1; AKT PN/subgroup 2; AKT
MES/subgroup 3;
AKT CLAS/subgroup 4; AKT SL/subgroup 5; AKT PROLIF/subgroup 6). Clinical and
molecular features of AKT subgroups are summarized in (A). Illustration of
proposed
neurodevelopmental cell of origin for AKT subgroups based on GO terms (B). ND
= not
determined.
Figure 9 depicts, in accordance with various embodiments of the invention,
consensus k-
means heat maps for k = 2 to 10 generated with AKT pathway genes in the
discovery dataset
(GBM195). Red indicates total consensus (consensus index of 1) while white
indicates no
consensus (consensus index of 0).
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Figure 10 depicts, in accordance with various embodiments of the invention,
average
expression of AKT pathway genes in subgroups. Hierarchical clustering using
AKT pathway
genes was used to group GBM patients and genes in the discovery (GBM 195)
dataset. Tumors
in the validation dataset were grouped by AKT class keeping the same order of
genes. The
expression of AKT pathway genes in each class was averaged and is shown as a
heatmap; red
and green respectively represent high/increased and low/decreased average
expression relative to
the median of all tumors. Black represents minimal expression difference
relative to the median
of all tumors.
Figure 11 depicts, in accordance with various embodiments of the invention,
Log2
(tumor/normal) DNA copy number in subgroups. Amplifications (red) and
deletions (blue) in
subgroups (y axis) were determined by segmentation analysis of normalized
signal intensities
from TCGA SNP arrays using GISTIC and viewed with IGV by chromosomal location
(x axis).
Figure 12 depicts, in accordance with various embodiments of the invention,
distribution
of clinical and molecular information by subgroup in the discovery dataset
(GBM195). The table
lists the number of tumors with the specified feature in each subgroup in the
discovery dataset.
Features with statistically significant enrichment in a subgroup after
Bonferroni correction (p <
0.05) are highlighted.
Figure 13 depicts, in accordance with various embodiments of the invention,
distribution
of clinical and molecular information by subgroup in the validation dataset
(TCGA). The table
lists the number of tumors with the specified feature in each subgroup in the
validation dataset.
Features with statistically significant enrichment in a subgroup after
Bonferroni correction (p <
0.05) are highlighted in dark grey. Features with statistically significant
enrichment in a
subgroup before Bonferroni correction are highlighted in light grey.
Figure 14 depicts, in accordance with various embodiments of the invention,
focal DNA
amplifications in subgroups. Copy number alterations in subgroups were
evaluated using
GISTIC and the q score for statistically significant focal DNA copy number
gains (q score <
0.25) listed. Focal copy number changes common to all subgroups (q < 0.25 in
all subgroups) are
not reported.
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Figure 15 depicts, in accordance with various embodiments of the invention,
focal DNA
deletions in subgroups. Copy number alterations in subgroups were evaluated
using GISTIC and
the q score for statistically significant focal DNA copy number losses (q
score < 0.25) are listed.
Focal copy number changes common to all subgroups (q < 0.25 in all subgroups)
are not
reported.
Figure 16 depicts, in accordance with various embodiments of the invention,
median
expression values of AKT pathway genes in each AKT cancer subgroup in the
discovery dataset
corresponding to the heatmap in Figure 10.
DETAILED DESCRIPTION OF THE INVENTION
All references cited herein are incorporated by reference in their entirety as
though fully
set forth. Unless defined otherwise, technical and scientific terms used
herein have the same
meaning as commonly understood by one of ordinary skill in the art to which
this invention
belongs. Allen et al., Remington: The Science and Practice of Pharmacy 22nd
ed.,
Pharmaceutical Press (September 15, 2012); Hornyak et al., Introduction to
Nanoscience and
Nanotechnology, CRC Press (2008); Singleton and Sainsbury, Dictionary of
Microbiology and
Molecular Biology 3rd ed., revised ed., J. Wiley & Sons (New York, NY 2006);
Smith, March's
Advanced Organic Chemistry Reactions, Mechanisms and Structure 7th ed., J.
Wiley & Sons
(New York, NY 2013); Singleton, Dictionary of DNA and Genome Technology 3rd
ed., Wiley-
Blackwell (November 28, 2012); and Green and Sambrook, Molecular Cloning: A
Laboratory
Manual 4th ed., Cold Spring Harbor Laboratory Press (Cold Spring Harbor, NY
2012), provide
one skilled in the art with a general guide to many of the terms used in the
present application.
For references on how to prepare antibodies, see Greenfield, Antibodies A
Laboratory Manual
2nd ed., Cold Spring Harbor Press (Cold Spring Harbor NY, 2013); Kohler and
Milstein,
Derivation of specific antibody-producing tissue culture and tumor lines by
cell fusion, Eur. J.
Immunol. 1976 Jul, 6(7):511-9; Queen and Selick, Humanized immunoglobulins, U.
S. Patent
No. 5,585,089 (1996 Dec); and Riechmann et al., Reshaping human antibodies for
therapy,
Nature 1988 Mar 24, 332(6162):323-7.
One skilled in the art will recognize many methods and materials similar or
equivalent to
those described herein, which could be used in the practice of the present
invention. Other
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features and advantages of the invention will become apparent from the
following detailed
description, taken in conjunction with the accompanying drawings, which
illustrate, by way of
example, various features of embodiments of the invention. Indeed, the present
invention is in no
way limited to the methods and materials described. For convenience, certain
terms employed
herein, in the specification, examples and appended claims are collected here.
Unless stated otherwise, or implicit from context, the following terms and
phrases include
the meanings provided below. Unless explicitly stated otherwise, or apparent
from context, the
terms and phrases below do not exclude the meaning that the term or phrase has
acquired in the
art to which it pertains. Unless otherwise defined, all technical and
scientific terms used herein
have the same meaning as commonly understood by one of ordinary skill in the
art to which this
invention belongs. It should be understood that this invention is not limited
to the particular
methodology, protocols, and reagents, etc., described herein and as such can
vary. The
definitions and terminology used herein are provided to aid in describing
particular
embodiments, and are not intended to limit the claimed invention, because the
scope of the
invention is limited only by the claims.
As used herein the term "comprising" or "comprises" is used in reference to
compositions, methods, and respective component(s) thereof, that are useful to
an embodiment,
yet open to the inclusion of unspecified elements, whether useful or not. It
will be understood by
those within the art that, in general, terms used herein are generally
intended as "open" terms
(e.g., the term "including" should be interpreted as "including but not
limited to," the term
"having" should be interpreted as "having at least," the term "includes"
should be interpreted as
"includes but is not limited to," etc.).
Unless stated otherwise, the terms "a" and "an" and "the" and similar
references used in
the context of describing a particular embodiment of the application
(especially in the context of
claims) can be construed to cover both the singular and the plural. The
recitation of ranges of
values herein is merely intended to serve as a shorthand method of referring
individually to each
separate value falling within the range. Unless otherwise indicated herein,
each individual value
is incorporated into the specification as if it were individually recited
herein. All methods
described herein can be performed in any suitable order unless otherwise
indicated herein or
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otherwise clearly contradicted by context. The use of any and all examples, or
exemplary
language (for example, "such as") provided with respect to certain embodiments
herein is
intended merely to better illuminate the application and does not pose a
limitation on the scope
of the application otherwise claimed. The abbreviation, "e.g." is derived from
the Latin exempli
gratia, and is used herein to indicate a non-limiting example. Thus, the
abbreviation "e.g." is
synonymous with the term "for example." No language in the specification
should be construed
as indicating any non-claimed element essential to the practice of the
application.
As used herein, the terms "treat," "treatment," "treating," or "amelioration"
when used in
reference to a disease, disorder or medical condition, refer to both
therapeutic treatment and
prophylactic or preventative measures, wherein the object is to prevent,
reverse, alleviate,
ameliorate, inhibit, lessen, slow down or stop the progression or severity of
a symptom or
condition. The term "treating" includes reducing or alleviating at least one
adverse effect or
symptom of a condition. Treatment is generally "effective" if one or more
symptoms or clinical
markers are reduced. Alternatively, treatment is "effective" if the
progression of a disease,
disorder or medical condition is reduced or halted. That is, "treatment"
includes not just the
improvement of symptoms or markers, but also a cessation or at least slowing
of progress or
worsening of symptoms that would be expected in the absence of treatment.
Also, "treatment"
may mean to pursue or obtain beneficial results, or lower the chances of the
individual
developing the condition even if the treatment is ultimately unsuccessful.
Those in need of
treatment include those already with the condition as well as those prone to
have the condition or
those in whom the condition is to be prevented.
"Beneficial results" or "desired results" may include, but are in no way
limited to,
lessening or alleviating the severity of the disease condition, preventing the
disease condition
from worsening, curing the disease condition, preventing the disease condition
from developing,
lowering the chances of a patient developing the disease condition, decreasing
morbidity and
mortality, and prolonging a patient's life or life expectancy. As non-limiting
examples,
"beneficial results" or "desired results" may be alleviation of one or more
symptom(s),
diminishment of extent of the deficit, stabilized (i.e., not worsening) state
of a tumor, delay or
slowing of a tumor, and amelioration or palliation of symptoms associated with
a tumor.
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"Disorders", "diseases", "conditions" and "disease conditions," as used herein
may
include, but are in no way limited to any form of malignant neoplastic cell
proliferative disorders
or diseases. Examples of such disorders include but are not limited to cancer
and tumor.
A "cancer" or "tumor" as used herein refers to an uncontrolled growth of cells
which
interferes with the normal functioning of the bodily organs and systems,
and/or all neoplastic cell
growth and proliferation, whether malignant or benign, and all pre-cancerous
and cancerous cells
and tissues. A subject that has a cancer or a tumor is a subject having
objectively measurable
cancer cells present in the subject's body. Included in this definition are
benign and malignant
cancers, as well as dormant tumors or micrometastasis. Cancers which migrate
from their
original location and seed vital organs can eventually lead to the death of
the subject through the
functional deterioration of the affected organs. As used herein, the term
"invasive" refers to the
ability to infiltrate and destroy surrounding tissue. Examples of cancer
include, but are not
limited to, nervous system tumor, nerve sheath tumor, and brain tumor or
cancer. Examples of
brain tumor include, but are not limited to, benign brain tumor, malignant
brain tumor, primary
brain tumor, secondary brain tumor, metastatic brain tumor, glioma,
glioblastoma multiforme
(GBM), medulloblastoma, ependymoma, astrocytoma, pilocytic astrocytoma,
oligodendroglioma, brainstem glioma, optic nerve glioma, mixed glioma such as
oligoastrocytoma, low-grade glioma, high-grade glioma, supratentorial glioma,
infratentorial
glioma, pontine glioma, meningioma, pituitary adenoma, and nerve sheath tumor.
Nervous
system tumor or nervous system neoplasm refers to any tumor affecting the
nervous system. A
nervous system tumor can be a tumor in the central nervous system (CNS), in
the peripheral
nervous system (PNS), or in both CNS and PNS. Examples of nervous system tumor
include but
are not limited to brain tumor, nerve sheath tumor, and optic nerve glioma.
As used herein, the term "administering," refers to the placement an agent as
disclosed
herein into a subject by a method or route which results in at least partial
localization of the
agents at a desired site. "Route of administration" may refer to any
administration pathway
known in the art, including but not limited to aerosol, nasal, oral,
transmucosal, transdermal,
parenteral, enteral, topical or local. "Parenteral" refers to a route of
administration that is
generally associated with injection, including intracranial, intraventricular,
intrathecal, epidural,
intradural, intraorbital, infusion, intraarterial, intracapsular,
intracardiac, intradermal,
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intramuscular, intraperitoneal, intrapulmonary, intraspinal, intrasternal,
intrathecal, intrauterine,
intravenous, subarachnoid, subcapsular, subcutaneous, transmucosal, or
transtracheal. Via the
parenteral route, the compositions may be in the form of solutions or
suspensions for infusion or
for injection, or as lyophilized powders. Via the enteral route, the
pharmaceutical compositions
can be in the form of tablets, gel capsules, sugar-coated tablets, syrups,
suspensions, solutions,
powders, granules, emulsions, microspheres or nanospheres or lipid vesicles or
polymer vesicles
allowing controlled release. Via the topical route, the pharmaceutical
compositions can be in the
form of aerosol, lotion, cream, gel, ointment, suspensions, solutions or
emulsions. In accordance
with the present invention, "administering" can be self-administering. For
example, it is
considered as "administering" that a subject consumes a composition as
disclosed herein.
The term "sample" or "biological sample" as used herein denotes a sample taken
or
isolated from a biological organism, e.g., a tumor sample from a subject.
Exemplary biological
samples include, but are not limited to, cheek swab; mucus; whole blood,
blood, serum; plasma;
urine; saliva; semen; lymph; fecal extract; sputum; other body fluid or
biofluid; cell sample;
tissue sample; tumor sample; and/or tumor biopsy etc. The term also includes a
mixture of the
above-mentioned samples. The term "sample" also includes untreated or
pretreated (or pre-
processed) biological samples. In some embodiments, a sample can comprise one
or more cells
from the subject. In some embodiments, a sample can be a tumor cell sample,
e.g. the sample
can comprise cancerous cells, cells from a tumor, and/or a tumor biopsy.
As used herein, a "subject" means a human or animal. Usually the animal is a
vertebrate
such as a primate, rodent, domestic animal or game animal. Primates include
chimpanzees,
cynomologous monkeys, spider monkeys, and macaques, e.g., Rhesus. Rodents
include mice,
rats, woodchucks, ferrets, rabbits and hamsters. Domestic and game animals
include cows,
horses, pigs, deer, bison, buffalo, feline species, e.g., domestic cat, and
canine species, e.g., dog,
fox, wolf. The terms, "patient", "individual" and "subject" are used
interchangeably herein. In
an embodiment, the subject is mammal. The mammal can be a human, non-human
primate,
mouse, rat, dog, cat, horse, or cow, but are not limited to these examples. In
addition, the
methods described herein can be used to treat domesticated animals and/or
pets.
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"Mammal" as used herein refers to any member of the class Mammalia, including,
without limitation, humans and nonhuman primates such as chimpanzees and other
apes and
monkey species; farm animals such as cattle, sheep, pigs, goats and horses;
domestic mammals
such as dogs and cats; laboratory animals including rodents such as mice, rats
and guinea pigs,
and the like. The term does not denote a particular age or sex. Thus, adult
and newborn
subjects, as well as fetuses, whether male or female, are intended to be
included within the scope
of this term.
A subject can be one who has been previously diagnosed with or identified as
suffering
from or having a condition in need of treatment (e.g., GBM) or one or more
complications
a) related to the condition, and optionally, have already undergone
treatment for the condition or
the one or more complications related to the condition. Alternatively, a
subject can also be one
who has not been previously diagnosed as having a condition or one or more
complications
related to the condition. For example, a subject can be one who exhibits one
or more risk factors
for a condition or one or more complications related to the condition or a
subject who does not
exhibit risk factors. A "subject in need" of treatment for a particular
condition can be a subject
suspected of having that condition, diagnosed as having that condition,
already treated or being
treated for that condition, not treated for that condition, or at risk of
developing that condition.
The term "statistically significant" or "significantly" refers to statistical
evidence that
there is a difference. It is defined as the probability of making a decision
to reject the null
hypothesis when the null hypothesis is actually true. The decision is often
made using the p-
value.
As used herein, "variants" can include, but are not limited to, those that
include
conservative amino acid mutations, SNP variants, splicing variants, degenerate
variants, and
biologically active portions of a gene. A "degenerate variant" as used herein
refers to a variant
that has a mutated nucleotide sequence, but still encodes the same polypeptide
due to the
redundancy of the genetic code.
The term "functional" when used in conjunction with "equivalent", "analog",
"derivative" or "variant" or "fragment" refers to an entity or molecule which
possess a biological
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activity that is substantially similar to a biological activity of the entity
or molecule of which it is
an equivalent, analog, derivative, variant or fragment thereof.
As used herein, the term "alkylating agents" refers to compounds and molecules
used in
cancer treatment that attach an alkyl group (C.H2.+1) to DNA. Examples of
alkylating agents
include but are not limited to nitrogen mustards such as cyclophosphamide,
mechlorethamine or
mustine (HN2), uramustine or uracil mustard, melphalan, chlorambucil,
ifosfamide, and
bendamustine; nitrosoureas such as carmustine (BCNU), lomustine (CCNU), and
streptozocinm;
alkyl sulfonates such busulfan; and thiotepa and its analogues.
As used herein, the term "PI3K/AKT/mTOR inhibitor" (also interchangeably
called as
PI3K/AKT/mTOR blocker, anti-PI3K/AKT/mTOR reagent, agent, drug or therapeutic,
) refers to
any reagent that inhibits the PI3K/AKT/mTOR signaling, including inhibition of
any molecular
signaling steps upstream or downstream of PI3K/AKT/mTOR. A PI3K/AKT/mTOR
inhibitor
can be a small molecule; a nucleic acid such as siRNA, shRNA, and miRNA; a
nucleic acid
analogue such as PNA, pc-PNA, and LNA; an aptamer; a ribosome; a peptide; a
protein; an
avimer; an antibody, or variants and fragments thereof. Examples of the
PI3K/AKT/mTOR
inhibitor include but are not limited to wortmannin, demethoxyviridin,
LY294002, perifosine,
idelalisib, PX-866, IPI-145, BAY 80-6946, BEZ235, RP6530, TGR 1202, SF1126,
INK1117,
GDC-0941, BKM120, XL147 (also known as 5AR245408), XL765 (also known as
5AR245409), Palomid, G5K1059615, Z5TK474, PWT33597, IC87114, TG100-115,
CAL263,
RP6503, PI-103, GNE-477, CUDC-907, and AEZS-136; VQD-002, miltefosine, and
AZD5363;
rapamycin, temsirolimus, evirolimus, ridaforolimus, epigallocatechin gallate
(EGCG), caffeine,
curcumin, and resveratrol.
As used herein, the term "IDH" means isocitrate dehydrogenase. SEQ ID NO:1
sets forth
one non-limiting example of an IDH1 gene sequence. As further disclosed
herein, to
characterize subgroups, the inventors found the distribution for alterations
in glioma-associated
genes in subgroups. It was found that subgroup 5 was enriched in tumors with
IDH mutations.
For example, IDH mutations in glioma may be found at arginine 132 (R132)
residue of isocitrate
dehydrogenase I (IDH1) or the R172 residue of IDH2. SEQ ID NO:2 sets forth one
non-limiting
example of an IDH1 sequence, that is, the cDNA sequence of one variant of
IDH1. SEQ ID
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NO:3 sets forth another non-limiting example of an IDH1 sequence, that is, the
cDNA sequence
of another variant of IDH1. SEQ ID NO:4 sets forth one non-limiting example of
an IDH2 gene
sequence.
For cancers such as GBM, many ineffective therapies can result from
classifying the
disease too generally. However, variations in natural history and therapeutic
response, as well as
molecular profiling, suggest that there could be molecular subtypes beyond the
standard
classifications. The ramifications are not insignificant. For example, the
failure to classify GBM
subtypes can affect patient treatment, drug development and clinical trials.
Clinical trials that do
not stratify for subgroups are underpowered and could miss subtype-specific
drugs.
Furthermore, unstratified patients may bear extra expense and toxicity.
Targets within a
subgroup might be missed if GBM are considered as a whole. The PI3K/Akt
pathway is one of
the 3 core pathways consistently altered in GBM. It often leads to activation
of Akt. Akt is an
oncogenic serine/threonine kinase that regulates metabolism, survival,
autophagy, proliferation,
migration, epithelial to mesenchymal (EMT) transition and angiogenesis. The
pathway is a large
and complex with many regulators, activators, effectors and feedback loops.
As disclosed herein, the inventors investigated PI3K/Akt/mTOR signaling
variations in
Akt subgroups, providing therapeutic alternatives for glioblastoma. The
GFR/PI3K/Akt pathway
is an important therapeutic target in glioblastoma (GB), but in the past,
response to pathway
inhibitors in clinical trials has been lackluster. The inventors examined
whether AKT pathway
variations contribute to poor response, and classified GBM based on AKT
pathway genes. There
were at least 5 GBM AKT subgroups. They were concordant with other found
subgroups but
subdivided them further to give new groups with distinct features. AKT
subgroups had different
molecular alterations and median survival. Importantly, the results
demonstrated that there is a
subset of GB patients sensitive to alkylating agent, and AKT classification
can identify them.
Akt classification also identified two subgroups enriched in IDH1 mutations
with different
clinical courses and molecular alterations. To characterize subgroups, the
inventor found the
distribution for alterations in glioma-associated genes in subgroups, and
found subgroup 5 was
enriched in tumors with IDH1 mutations. These data suggest AKT classification
is a biomarker
for sensitivity to alkylating agents and PI3K/AKT pathway inhibitors. The
results advance
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molecular classification of GB and can be used to stratify patients for
clinical trials and enhance
discovery of class-specific therapeutic targets.
As further disclosed herein, it was found that there was a statistically
significant
enrichment of IDH1 mutations in the AKT subgroup 5 cluster. Many IDH mutations
in glioma
are found at arginine 132 (R132) residue of isocitrate dehydrogenase I (IDH1)
or the R172
residue of IDH2. There was also evidence found that the AKT subgroup 5
patients as described
herein were particularly sensitive to alkylating agents.
In another embodiment, the present invention provides a method of diagnosing a
cancer
subtype in a subject comprising obtaining a sample from the subject, assaying
the sample to
determine an AKT expression profile, and diagnosing the cancer subtype based
on the AKT
expression profile. In another embodiment, the cancer is GBM. In another
embodiment, the
subject is human. In another embodiment, the subtype is characterized by a
cluster defined by
the distribution of alterations in glioma associated genes. In one embodiment,
the AKT
expression profile is defined by a cluster of distribution of alterations in
glioma associated genes
in the AKT signaling pathway. In one embodiment, wherein the AKT expression
profile is made
up of one or more genetic loci listed in Table 2. In one embodiment, the
cancer subtype is a
cancer subtype of GBM. In one embodiment, the cancer subtype includes the
presence of tumors
enriched with one or more IDH1 and/or IDH2 mutations.
In one embodiment, the present invention provides a method of diagnosing a
cancer
subtype in a subject comprising obtaining a sample from the subject, assaying
the sample to
determine the presence or absence of IDH1 and/or IDH2 mutations, and
diagnosing the cancer
subtype based on the presence of IDH1 and/or IDH2 mutations. In another
embodiment, the
cancer is GBM. In one embodiment, the individual is a human. In another
embodiment, the
presence of one or more IDH1 and/or IDH2 mutations relative to a normal
individual is
indicative of the cancer subtype AKT subgroup 5.
In another embodiment, the present invention provides a method of prognosing
GBM
disease by diagnosing a GBM disease subtype based on the AKT expression
profile, and
determining the severity of the disease based on the GBM disease subtype.
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In one embodiment, the present invention provides for a method of treating a
subject for
cancer comprising obtaining a sample from the subject, assaying the sample to
determine a
cancer subtype based on what is the AKT expression profile, and treating the
subject. In another
embodiment, the cancer is GBM. In another embodiment, the subject is human. In
another
embodiment, the subtype is characterized by a cluster defined by the
distribution of alterations in
glioma associated genes. In another embodiment, the treatment comprises
administering a
therapeutically effective dosage of a composition comprising one or more
alkylating agents to
the individual. In another embodiment, the treatment comprises administering a
therapeutically
effective dosage of a composition comprising one or more PI3K/Akt/mTOR
inhibitors to the
individual.
In one embodiment, the present invention provides for a method of treating GBM
in a
subject comprising obtaining a sample from the subject, assaying the sample to
diagnose a GBM
subtype based on the presence of an AKT expression profile, and treating the
subject. In some
embodiments, the AKT subgroup includes the presence of one or more IDH1 and/or
IDH2
mutations. In another embodiment, the present invention provides a method of
treating an
individual for cancer by obtaining a sample from the individual, assaying the
sample to
determine the presence of one or more IDH1 and/or IDH2 mutations, and treating
the individual.
In another embodiment, treating the individual comprises administration of a
therapeutically
effective dosage of a composition comprising one or more alkylating agents to
the individual.
In various embodiments, the one or more IDH1 mutations include mutation of
arginine
132 (R132) residue of isocitrate dehydrogenase I (IDH1). In various
embodiments, the one or
more IDH2 mutations include the mutation of arginine 172 (R172) residue of
IDH2. In various
embodiments, assaying the sample includes determining the presence of a GBM
tumor enriched
with one or more IDH1 and/or IDH2 mutations.
Activity of GFR/PI3K/AKT pathway inhibitors in glioblastoma clinical trials
has not
been robust. While not wishing to be bound by any theory, the inventors
believe that variations
in the pathway between tumors contribute to poor response. The inventors
clustered GBM based
on AKT pathway genes and discovered new subtypes then characterized their
clinical and
molecular features. There are at least 5 GBM AKT subtypes having distinct DNA
copy number
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alterations, enrichment in oncogenes and tumor suppressor genes and patterns
of expression for
PI3K/AKT/mTOR signaling components. Gene Ontology terms indicate a different
cell of origin
or dominant phenotype for each subgroup. Evidence suggests one subtype is very
sensitive to
BCNU or CCNU (median survival 5.8 vs. 1.5 years; BCNU/CCNU vs other
treatments;
respectively). AKT subtyping advances previous approaches by revealing
additional subgroups
with unique clinical and molecular features. Evidence indicates it is a
predictive marker for
response to BCNU or CCNU and PI3K/AKT/mTOR pathway inhibitors. The inventors
demonstrate that Akt subtyping helps stratify patients for clinical trials and
augments discovery
of class-specific therapeutic targets.
Classification and Diagnosis Methods
In various embodiments, the present invention provides a method for
classifying a cancer
in a subject. The method may consist of or may consist essentially of or may
comprise:
obtaining a biological sample from the subject; determining an expression
pattern of AKT
pathway components in the biological sample; and classifying the cancer based
on the
determined expression pattern of AKT pathway components in the biological
sample. In various
embodiments, said classifying comprises classifying the cancer into Cl, PN,
MES, CLAS, SL, or
PROLIF subtype if the biological sample's expression pattern of AKT pathway
components is
determined to be Cl, PN, MES, CLAS, SL, or PROLIF subtype's expression pattern
of AKT
pathway components. Non-limiting examples of Cl, PN, MES, CLAS, SL, or PROLIF
subtype's expression pattern of AKT pathway components may be found in Figure
10.
In various embodiments, the present invention provides a method for diagnosing
whether
a subject has a cancer subtype. The method may consist of or may consist
essentially of or may
comprise: obtaining a biological sample from the subject; determining whether
an expression
pattern of AKT pathway components is present in the biological sample; and
diagnosing the
subject as having the cancer subtype if the expression pattern of AKT pathway
components is
determined to be present in the biological sample. In various further
embodiments, the method
comprises administering a therapeutically effective amount of a therapeutic to
the subject,
thereby treating, preventing, reducing the likelihood of having, reducing the
severity of and/or
slowing the progression of the cancer subtype. In some embodiments, the cancer
subtype is Cl,
PN, MES, CLAS, SL, or PROLIF subtype. In various embodiments, the expression
pattern is
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Cl, PN, MES, CLAS, SL, or PROLIF subtype's expression pattern of AKT pathway
components.
In various embodiments, the cancer is a brain tumor, glioma, or GBM. In
various
embodiments, the subject is a human. In various embodiments, the subject is a
mammalian
subject including but not limited to human, monkey, ape, dog, cat, cow, horse,
goat, pig, rabbit,
mouse and rat. In various embodiments, the biological sample comprises a cell,
neuron, glia,
brain cell, spinal cord cell, brain neuron, brain glia, spinal cord neuron, or
spinal cord glia, or a
combination thereof. In some embodiments, the biological sample comprises a
tumor cell or
tissue. In some embodiments, the biological sample comprises a tumor biopsy or
sample.
In various embodiments, the AKT pathway components comprise one classifier
listed in
Table 2. In various embodiments, the AKT pathway components comprise two
classifiers listed
in Table 2. In various embodiments, the AKT pathway components comprise three
classifiers
listed in Table 2. In various embodiments, the AKT pathway components comprise
four
classifiers listed in Table 2. In various embodiments, the AKT pathway
components comprise
five or more classifiers listed in Table 2. In various embodiments, the AKT
pathway
components comprise all classifiers listed in Table 2.
In various embodiments, the AKT pathway components comprise ACLY, AKT1,
ATXN1, BCL10, CCND1, CDC37, CDKN1A, CDKN1B, CFD, CHEK1, EGFR, EIF3B, EIF3E,
EIF3G, EIF3H, EIF4EBP1, EPAS1, EZH2, FGFR2, FGFR3, FOX03, FYN, GAB1, GAB2,
GRB10, GSK3B, HIF1A, HSP90AB1, HSP90B1, INPP5D, IRS1, IRS2, KDR, KRAS,
MAP3K5, MAPK8IP1, NRAS, PALLD, PDGFA, PDGFC, PDGFD, PDGFRB, PDK1, PHLPP1,
PIK3C2B, PIK3CA, PIK3R1, PKD2, PKN2, PPARGC1A, PPP2R1A, PPP2R2B, RAF1,
SORBS2, SRSF1, SSB, SYK, TP53, TRIB3, TSC1, TSC2, TWIST1, VIM, and/or WNK1, or
a
combination thereof.
In various embodiments, said determining is performed by: contacting the
biological
sample with one or more detection agents that specifically bind to one or more
AKT pathway
components; and detecting the level of binding between the one or more
detection agents and the
one or more AKT pathway components. In some embodiments, the one or more
detection agents
are oligonucleotide probes, nucleic acids, DNAs, RNAs, peptides, proteins,
antibodies, aptamers,
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or small molecules, or a combination thereof. In various embodiments, said
detecting is
performed by using a microarray. In some embodiments, the microarray is an
oligonucleotide
microarray, DNA microarray, cDNA microarrays, RNA microarray, peptide
microarray, protein
microarray, or antibody microarray, or a combination thereof.
In various embodiments, the method further comprises selecting, choosing or
prescribing
a therapeutic for the subject after diagnosis. In various embodiments, the
method further
comprises instructing or directing the subject to receive a therapeutic after
diagnosis. In various
embodiments, the method further comprises administering a therapeutically
effective amount of
a therapeutic to the subject, thereby treating, preventing, reducing the
likelihood of having,
reducing the severity of and/or slowing the progression of the diagnosed
cancer subtype.
Treatment Methods
In various embodiments, the present invention provides a method for treating,
preventing,
reducing the likelihood of having, reducing the severity of and/or slowing the
progression of a
cancer subtype in a subject. The method may consist of or may consist
essentially of or may
comprise: obtaining a biological sample from the subject; determining whether
an expression
pattern of AKT pathway components is present in the biological sample;
providing a therapeutic;
and administering a therapeutically effective amount of the therapeutic to the
subject if the
expression pattern of AKT pathway components is determined to be present in
the biological
sample, thereby treating, preventing, reducing the likelihood of having,
reducing the severity of
and/or slowing the progression of the cancer subtype. In some embodiments, the
cancer subtype
is Cl, PN, MES, CLAS, SL, or PROLIF subtype. In various embodiments, the
expression
pattern is Cl, PN, MES, CLAS, SL, or PROLIF subtype's expression pattern of
AKT pathway
components. Non-limiting examples of Cl, PN, MES, CLAS, SL, or PROLIF
subtype's
expression pattern of AKT pathway components may be found in Figure 10.
In various embodiments, the present invention provides a method for treating,
preventing,
reducing the likelihood of having, reducing the severity of and/or slowing the
progression of SL
cancer subtype in a subject. The method may consist of or may consist
essentially of or may
comprise: obtaining a biological sample from the subject; determining whether
SL subtype's
expression pattern of AKT pathway components is present in the biological
sample; providing a
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therapeutic; and administering a therapeutically effective amount of the
therapeutic to the subject
if SL subtype's expression pattern of AKT pathway components is determined to
be present in
the biological sample, thereby treating, preventing, reducing the likelihood
of having, reducing
the severity of and/or slowing the progression of SL cancer subtype.
In various embodiments, the present invention provides a method for treating
an AKT
cancer subtype in a subject. The method may consist of or may consist
essentially of or may
comprise: providing a therapeutic; and administering a therapeutically
effective amount of the
therapeutic to the subject, thereby treating the AKT cancer subtype in the
subject. In some
embodiments, the cancer subtype is Cl, PN, MES, CLAS, SL, or PROLIF subtype.
In various embodiments, the present invention provides a method for treating
SL cancer
subtype in a subject. The method may consist of or may consist essentially of
or may comprise:
providing a therapeutic; and administering a therapeutically effective amount
of the therapeutic
to the subject, thereby treating SL cancer subtype in the subject.
In various embodiments, the present invention provides a method for treating
an AKT
cancer subtype in a subject. The method comprises administering a
therapeutically effective
amount of the therapeutic to the subject who has been diagnosed with the AKT
cancer subtype,
thereby treating the AKT cancer subtype in the subject. In some embodiments,
the cancer
subtype is Cl, PN, MES, CLAS, SL, or PROLIF subtype. In some embodiments, the
subject has
been diagnosed with the AKT cancer subtype via methods as described in the
present invention.
In various embodiments, the method may further comprise providing the
therapeutic.
In various embodiments, the present invention provides a method for treating
SL cancer
subtype in a subject. The method comprises administering a therapeutically
effective amount of
the therapeutic to the subject who has been diagnosed with the SL cancer
subtype, thereby
treating the SL cancer subtype in the subject. In some embodiments, the
subject has been
diagnosed with the SL cancer subtype via methods as described in the present
invention. In
various embodiments, the method may further comprise providing the
therapeutic.
In various embodiments, the present invention provides a method for treating
an AKT
cancer subtype in a subject. The method comprises ordering a diagnostic test
to determine if the
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subject has an AKT cancer subtype; and administering a therapeutically
effective amount of the
therapeutic to the subject who has been diagnosed with the AKT cancer subtype,
thereby treating
the AKT cancer subtype in the subject. In some embodiments, the diagnostic
test is performed
via methods as described in the present invention. In some embodiments, the
cancer subtype is
Cl, PN, MES, CLAS, SL, or PROLIF subtype. In various embodiments, the method
may further
comprise providing the therapeutic.
In various embodiments, the present invention provides a method for treating
SL cancer
subtype in a subject. The method comprises ordering a diagnostic test to
determine if the subject
has SL cancer subtype; and administering a therapeutically effective amount of
the therapeutic to
the subject who has been diagnosed with the SL cancer subtype, thereby
treating the SL cancer
subtype in the subject. In some embodiments, the diagnostic test is performed
via methods as
described in the present invention. In various embodiments, the method may
further comprise
providing the therapeutic.
In various embodiments, the cancer is a brain tumor, glioma, or GBM. In
various
embodiments, the subject is a human. In various embodiments, the subject is a
mammalian
subject including but not limited to human, monkey, ape, dog, cat, cow, horse,
goat, pig, rabbit,
mouse and rat. In various embodiments, the biological sample comprises a cell,
neuron, glia,
brain cell, spinal cord cell, brain neuron, brain glia, spinal cord neuron, or
spinal cord glia, or a
combination thereof. In some embodiments, the biological sample comprises a
tumor cell or
tissue. In some embodiments, the biological sample comprises a tumor biopsy or
sample.
In various embodiments, the therapeutic is a nucleic acid, DNA, RNA, peptide,
protein,
antibody, aptamer, or small molecule, or a combination thereof. In some
embodiments, the
therapeutic is an alkylating agent, or a PI3K/AKT/mTOR inhibitor, or a
combination thereof. In
certain embodiments, the therapeutic is BCNU or CCNU, a functional equivalent,
analog,
derivative or salt of BCNU or CCNU, or a combination thereof.
Typical dosages of an effective amount of the therapeutic can be in the ranges
recommended by the manufacturer where known therapeutic molecules or compounds
are used,
and also as indicated to the skilled artisan by the in vitro responses in
cells or in vivo responses in
animal models. Such dosages typically can be reduced by up to about an order
of magnitude in
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concentration or amount without losing relevant biological activity. The
actual dosage can
depend upon the judgment of the physician, the condition of the patient, and
the effectiveness of
the therapeutic method based, for example, on the in vitro responsiveness of
relevant cultured
cells or histocultured tissue sample, or the responses observed in the
appropriate animal models.
In various embodiments, the therapeutic may be administered once a day
(SID/QD), twice a day
(BID), three times a day (TID), four times a day (QID), or more, so as to
administer an effective
amount of the therapeutic to the subject, where the effective amount is any
one or more of the
doses described herein.
In various embodiments, the therapeutic is administered at about 0.001-0.01,
0.01-0.1,
0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-200, 200-300, 300-400, 400-
500, 500-600, 600-
700, 700-800, 800-900, or 900-1000 mg/m2, or a combination thereof. In various
embodiments,
the therapeutic is administered at about 0.001-0.01, 0.01-0.1, 0.1-0.5, 0.5-5,
5-10, 10-20, 20-50,
50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-
900, or 900-1000
mg/kg, or a combination thereof. In various embodiments, the therapeutic is
administered once,
twice, three or more times. In various embodiments, the therapeutic is
administered about 1-3
times per day, 1-7 times per week, 1-9 times per month, or 1-12 times per
year. In various
embodiments, the therapeutic is administered for about 1-10 days, 10-20 days,
20-30 days, 30-40
days, 40-50 days, 50-60 days, 60-70 days, 70-80 days, 80-90 days, 90-100 days,
1-6 months, 6-
12 months, or 1-5 years. Here, "mg/kg" refers to mg per kg body weight of the
subject, and
"mg/m2" refers to mg per m2 body surface area of the subject. In certain
embodiments, the
therapeutic is administered to a human. In certain embodiments, the
therapeutic is BCNU or
CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or
a combination
thereof.
In various embodiments, the effective amount of the therapeutic is any one or
more of
about 0.001-0.01, 0.01-0.1, 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-
200, 200-300, 300-
400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 pg/kg/day, or a
combination
thereof. In various embodiments, the effective amount of the therapeutic is
any one or more of
about 0.001-0.01, 0.01-0.1, 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-
200, 200-300, 300-
400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 pg/m2/day, or a
combination
thereof. In various embodiments, the effective amount of the therapeutic is
any one or more of
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about 0.001-0.01, 0.01-0.1, 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-
200, 200-300, 300-
400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 mg/kg/day, or a
combination
thereof. In various embodiments, the effective amount of the therapeutic is
any one or more of
about 0.001-0.01, 0.01-0.1, 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-
200, 200-300, 300-
400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 mg/m2/day, or a
combination
thereof. Here, "pg/kg/day" or "mg/kg/day" refers to pg or mg per kg body
weight of the subject
per day, and "pg/m2/day" or "mg/m2/day" refers to pg or mg per m2 body surface
area of the
subject per day.
In some embodiments, the therapeutic may be administered at the prevention
stage of a
condition (i.e., when the subject has not developed the condition but is
likely to or in the process
to develop the condition). In other embodiments, the therapetuic may be
administered at the
treatment stage of a condition (i.e., when the subject has already developed
the condition). As a
non-limiting example, the target condition is GBM. In this exemplar situation,
the patient may
be treated with the methods described herein when the patient has not yet
developed GBM, or is
likely to develop GBM, or is in the process of developing GBM, or has already
developed GBM.
In accordance with the invention, the therapeutic may be administered using
the
appropriate modes of administration, for instance, the modes of administration
recommended by
the manufacturer for each of the therapeutic. In accordance with the
invention, various routes
may be utilized to administer the therapeutic of the claimed methods,
including but not limited to
aerosol, nasal, oral, transmucosal, transdermal, parenteral, enteral, topical,
local, implantable
pump, continuous infusion, capsules and/or injections. In various embodiments,
the therapeutic
is administered intracranially, intraventricularly, intrathecally, epidurally,
intradurally, topically,
intravascularly, intravenously, intraarterially, intratumorally,
intramuscularly, subcutaneously,
intraperitoneally, intranasally, or orally.
In various embodiments, the therapeutic is provided as a pharmaceutical
composition. In
various embodiments, the composition is formulated for via any route of
administration,
including but not limited to intracranial, intraventricular, intrathecal,
epidural, intradural, topical,
intravascular, intravenous, intraarterial, intratumoral, intramuscular,
subcutaneous,
intraperitoneal, intranasal or oral administration. Methods for these
administrations are known to
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one skilled in the art. Preferred pharmaceutical compositions will also
exhibit minimal toxicity
when administered to a mammal.
In various embodiments, the pharmaceutical compositions according to the
invention can
contain any pharmaceutically acceptable excipient. "Pharmaceutically
acceptable excipient"
means an excipient that is useful in preparing a pharmaceutical composition
that is generally
safe, non-toxic, and desirable, and includes excipients that are acceptable
for veterinary use as
well as for human pharmaceutical use. Such excipients may be solid, liquid,
semisolid, or, in the
case of an aerosol composition, gaseous. Examples of excipients include but
are not limited to
starches, sugars, microcrystalline cellulose, diluents, granulating agents,
lubricants, binders,
disintegrating agents, wetting agents, emulsifiers, coloring agents, release
agents, coating agents,
sweetening agents, flavoring agents, perfuming agents, preservatives,
antioxidants, plasticizers,
gelling agents, thickeners, hardeners, setting agents, suspending agents,
surfactants, humectants,
carriers, stabilizers, and combinations thereof.
In various embodiments, the pharmaceutical compositions according to the
invention can
contain any pharmaceutically acceptable carrier. "Pharmaceutically acceptable
carrier" as used
herein refers to a pharmaceutically acceptable material, composition, or
vehicle that is involved
in carrying or transporting a compound of interest from one tissue, organ, or
portion of the body
to another tissue, organ, or portion of the body. For example, the carrier may
be a liquid or solid
filler, diluent, excipient, solvent, or encapsulating material, or a
combination thereof. Each
component of the carrier must be "pharmaceutically acceptable" in that it must
be compatible
with the other ingredients of the formulation. It must also be suitable for
use in contact with any
tissues or organs with which it may come in contact, meaning that it must not
carry a risk of
toxicity, irritation, allergic response, immunogenicity, or any other
complication that excessively
outweighs its therapeutic benefits.
The pharmaceutical compositions according to the invention can also be
encapsulated,
tableted or prepared in an emulsion or syrup for oral administration.
Pharmaceutically
acceptable solid or liquid carriers may be added to enhance or stabilize the
composition, or to
facilitate preparation of the composition. Liquid carriers include syrup,
peanut oil, olive oil,
glycerin, saline, alcohols and water. Solid carriers include starch, lactose,
calcium sulfate,
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dihydrate, terra alba, magnesium stearate or stearic acid, talc, pectin,
acacia, agar or gelatin. The
carrier may also include a sustained release material such as glyceryl
monostearate or glyceryl
distearate, alone or with a wax.
The pharmaceutical preparations are made following the conventional techniques
of
pharmacy involving dry milling, mixing, and blending for powder forms;
milling, mixing,
granulation, and compressing, when necessary, for tablet forms; or milling,
mixing and filling for
hard gelatin capsule forms. When a liquid carrier is used, the preparation
will be in the form of a
syrup, elixir, emulsion or an aqueous or non-aqueous suspension. Such a liquid
formulation may
be administered directly p.o. or filled into a soft gelatin capsule.
The pharmaceutical compositions according to the invention may be delivered in
a
therapeutically effective amount. The precise therapeutically effective amount
is that amount of
the composition that will yield the most effective results in terms of
efficacy of treatment in a
given subject. This amount will vary depending upon a variety of factors,
including but not
limited to the characteristics of the therapeutic compound (including
activity, pharmacokinetics,
pharmacodynamics, and bioavailability), the physiological condition of the
subject (including
age, sex, disease type and stage, general physical condition, responsiveness
to a given dosage,
and type of medication), the nature of the pharmaceutically acceptable carrier
or carriers in the
formulation, and the route of administration. One skilled in the clinical and
pharmacological arts
will be able to determine a therapeutically effective amount through routine
experimentation, for
instance, by monitoring a subject's response to administration of a compound
and adjusting the
dosage accordingly. For additional guidance, see Remington: The Science and
Practice of
Pharmacy (Gennaro ed. 20th edition, Williams & Wilkins PA, USA) (2000).
Before administration to patients, formulants may be added to the composition.
A liquid
formulation may be preferred. For example, these formulants may include oils,
polymers,
vitamins, carbohydrates, amino acids, salts, buffers, albumin, surfactants,
bulking agents or
combinations thereof.
Carbohydrate formulants include sugar or sugar alcohols such as
monosaccharides,
disaccharides, or polysaccharides, or water soluble glucans. The saccharides
or glucans can
include fructose, dextrose, lactose, glucose, mannose, sorbose, xylose,
maltose, sucrose, dextran,
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pullulan, dextrin, alpha and beta cyclodextrin, soluble starch, hydroxethyl
starch and
carboxymethylcellulose, or mixtures thereof. "Sugar alcohol" is defined as a
C4 to C8
hydrocarbon having an ¨OH group and includes galactitol, inositol, mannitol,
xylitol, sorbitol,
glycerol, and arabitol. These sugars or sugar alcohols mentioned above may be
used individually
or in combination. There is no fixed limit to amount used as long as the sugar
or sugar alcohol is
soluble in the aqueous preparation. In one embodiment, the sugar or sugar
alcohol concentration
is between 1.0 w/v % and 7.0 w/v %, more preferable between 2.0 and 6.0 w/v %.
Amino acids formulants include levorotary (L) forms of carnitine, arginine,
and betaine;
however, other amino acids may be added.
Polymers formulants include polyvinylpyrrolidone (PVP) with an average
molecular
weight between 2,000 and 3,000, or polyethylene glycol (PEG) with an average
molecular
weight between 3,000 and 5,000.
It is also preferred to use a buffer in the composition to minimize pH changes
in the
solution before lyophilization or after reconstitution. Most any physiological
buffer may be used
including but not limited to citrate, phosphate, succinate, and glutamate
buffers or mixtures
thereof. In some embodiments, the concentration is from 0.01 to 0.3 molar.
Surfactants that can
be added to the formulation are shown in EP Nos. 270,799 and 268,110.
Another drug delivery system for increasing circulatory half-life is the
liposome.
Methods of preparing liposome delivery systems are discussed in Gabizon et
at., Cancer
Research (1982) 42:4734; Cafiso, Biochem Biophys Acta (1981) 649:129; and
Szoka, Ann Rev
Biophys Eng (1980) 9:467. Other drug delivery systems are known in the art and
are described
in, e.g., Poznansky et at., DRUG DELIVERY SYSTEMS (R. L. Juliano, ed., Oxford,
N.Y.
1980), pp. 253-315; M. L. Poznansky, Pharm Revs (1984) 36:277.
After the liquid pharmaceutical composition is prepared, it may be lyophilized
to prevent
degradation and to preserve sterility. Methods for lyophilizing liquid
compositions are known to
those of ordinary skill in the art. Just prior to use, the composition may be
reconstituted with a
sterile diluent (Ringer's solution, distilled water, or sterile saline, for
example) which may
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include additional ingredients. Upon reconstitution, the composition is
administered to subjects
using those methods that are known to those skilled in the art.
The compositions of the invention may be sterilized by conventional, well-
known
sterilization techniques. The resulting solutions may be packaged for use or
filtered under
aseptic conditions and lyophilized, the lyophilized preparation being combined
with a sterile
solution prior to administration. The compositions may contain
pharmaceutically-acceptable
auxiliary substances as required to approximate physiological conditions, such
as pH adjusting
and buffering agents, tonicity adjusting agents and the like, for example,
sodium acetate, sodium
lactate, sodium chloride, potassium chloride, calcium chloride, and
stabilizers (e.g., 1-20%
maltose, etc.).
The pharmaceutical composition according to the invention can also be a bead
system for
delivering the therapeutic agent to the target cells. For example, pectin/zein
hydrogel bead
system may be used to deliver Neuregulin-4 or a pharmaceutical equivalent,
analog, derivative or
a salt thereof, to the target cells in the subject (Yan F. et al., J Clin
Invest. 2011 Jun;
121(6):2242-53).
Kits of the Invention
The present invention is also directed to a kit that is used to classify,
diagnose and/or treat
cancers. The kit is an assemblage of materials or components, including at
least one of the
inventive elements or modules. Thus, in some embodiments the kit contains one
or more
detection agents that specifically bind to one or more AKT pathway components,
as described
above; and in other embodiments the kit contains a cancer therapeutic, as
described above. In
certain embodiments the kit contains a composition including a drug delivery
molecule
complexed with a cancer therapeutic, as described above.
In various embodiments, the present invention provides a kit for classifying a
cancer in a
subject. The kit may consist of or may consist essentially of or may comprise:
one or more
detection agents that specifically bind to one or more AKT pathway components;
instructions for
using the one or more detection agents to classify the cancer in the subject.
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In various embodiments, the present invention provides a kit for diagnosing
whether a
subject has a cancer subtype. The kit may consist of or may consist
essentially of or may
comprise: one or more detection agents that specifically bind to one or more
AKT pathway
components; instructions for using the one or more detection agents to
diagnose whether a
subject has the cancer subtype.
In various embodiments, the present invention provides a kit for treating,
preventing,
reducing the likelihood of having, reducing the severity of and/or slowing the
progression of a
cancer subtype in a subject. The kit may consist of or may consist essentially
of or may
comprise: one or more detection agents that specifically bind to one or more
AKT pathway
components; a quantity of a therapeutic; and instructions for using the one or
more detection
agents and the therapeutic to treat, prevent, reduce the likelihood of having,
reduce the severity
of and/or slow the progression of the cancer subtype in the subject
In various embodiments, the present invention provides a kit for treating an
AKT cancer
subtype in a subject. The kit may consist of or may consist essentially of or
may comprise: a
quantity of a therapeutic; and instructions for using the therapeutic to treat
the AKT cancer
subtype in the subject.
In various embodiments, the subject is a human. In various embodiments, the
cancer is a
brain tumor, glioma, or GBM. In various embodiments, the cancer subtype is Cl,
PN, MES,
CLAS, SL, or PROLIF subtype.
In various embodiments, the one or more detection agents are applied to
contact a
biological sample obtained from the subject; and the level of binding between
the one or more
detection agents and the one or more AKT pathway components is detected to
determine
expression patterns of AKT pathway components. In some embodiments, the one or
more
detection agents are oligonucleotide probes, nucleic acids, DNAs, RNAs,
peptides, proteins,
antibodies, aptamers, or small molecules, or a combination thereof. In various
embodiments, the
level of binding is detected using a microarray. In some embodiments, the
microarray is an
oligonucleotide microarray, DNA microarray, cDNA microarrays, RNA microarray,
peptide
microarray, protein microarray, or antibody microarray, or a combination
thereof.
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In various embodiments, the therapeutic is a nucleic acid, DNA, RNA, peptide,
protein,
antibody, aptamer, or small molecule, or a combination thereof. In some
embodiments, the
therapeutic is an alkylating agent, or a PI3K/AKT/mTOR inhibitor, or a
combination thereof. In
certain embodiments, the therapeutic is BCNU or CCNU, a functional equivalent,
analog,
derivative or salt of BCNU or CCNU, or a combination thereof.
The exact nature of the components configured in the inventive kit depends on
its
intended purpose. In one embodiment, the kit is configured particularly for
the purpose of
treating mammalian subjects. In another embodiment, the kit is configured
particularly for the
purpose of treating human subjects. In further embodiments, the kit is
configured for veterinary
applications, treating subjects such as, but not limited to, farm animals,
domestic animals, and
laboratory animals.
Instructions for use may be included in the kit. "Instructions for use"
typically include a
tangible expression describing the technique to be employed in using the
components of the kit
to affect a desired outcome. Optionally, the kit also contains other useful
components, such as,
spray bottles or cans, diluents, buffers, pharmaceutically acceptable
carriers, syringes, catheters,
applicators (for example, applicators of cream, gel or lotion etc.), pipetting
or measuring tools,
bandaging materials or other useful paraphernalia as will be readily
recognized by those of skill
in the art.
The materials or components assembled in the kit can be provided to the
practitioner
stored in any convenient and suitable ways that preserve their operability and
utility. For
example the detection agents and/or cancer therapeutics can be in dissolved,
dehydrated, or
lyophilized form; they can be provided at room, refrigerated or frozen
temperatures. The
components are typically contained in suitable packaging material(s). As
employed herein, the
phrase "packaging material" refers to one or more physical structures used to
house the contents
of the kit, such as inventive compositions and the like. The packaging
material is constructed by
well-known methods, preferably to provide a sterile, contaminant-free
environment. The
packaging materials employed in the kit are those customarily utilized in
assays and therapies.
As used herein, the term "package" refers to a suitable solid matrix or
material such as glass,
plastic, paper, foil, and the like, capable of holding the individual kit
components. Thus, for
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example, a package can be a glass vial used to contain suitable quantities of
a composition as
described herein. The packaging material generally has an external label which
indicates the
contents and/or purpose of the kit and/or its components.
Compositions
The present invention is also directed to a composition that is used to
classify and/or
diagnose cancers and cancer subtyps.
In some embodiments, the composition comprises one or more detection agents
that
specifically bind to one or more AKT pathway components, as described herein;
and a biological
sample from a subject desiring a classification or diagnosis regarding a
cancer.
In various embodiments, the composition comprises one or more detection agents
that
specifically bind to one or more AKT pathway components; as described herein;
and a biological
sample from a subject desiring a classification regarding a cancer.
In various embodiments, the composition one or more detection agents that
specifically
bind to one or more AKT pathway components; and a biological sample from a
subject desiring
a subject diagnosis on whether he/she has the cancer subtype.
In various embodiments, the cancer subtype is Cl, PN, MES, CLAS, SL, or PROLIF
subtype.
Systems and Computers
In certain embodiments, the methods of the invention implement a computer
program to
calculate a copy number, copy number loss, copy number gain, LOH, mutation,
deletion and
expression levels. For example, a computer program can be used to perform the
algorithms
described herein. A computer system can also store and manipulate data
generated by the
methods of the present invention which comprises a plurality of hybridization
signal
changes/profiles during approach to equilibrium in different hybridization
measurements and
which can be used by a computer system in implementing the methods of this
invention. In
certain embodiments, a computer system receives probe hybridization data; (ii)
stores probe
hybridization data; and (iii) compares probe hybridization data to determine
the state of AKT
pathway components and genomic loci in a biological sample from cancerous or
pre-cancerous
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tissue. The copy number, copy number loss, copy number gain, LOH, mutation,
deletion and
expression levels is then calculated. In some embodiments, a computer system
(i) compares the
determined copy number, copy number loss, copy number gain, LOH, mutation,
deletion and
expression levels to a threshold value or reference value; and (ii) outputs an
indication of
whether said copy number, copy number loss, copy number gain, LOH, mutation,
deletion and
expression levels is above or below a threshold value, or a genetic signature
based on said
indication. In certain embodiments, such computer systems are also considered
part of the
present invention.
Numerous types of computer systems can be used to implement the analytic
methods of
1() this invention according to knowledge possessed by a skilled artisan in
the bioinformatics and/or
computer arts.
Several software components can be loaded into memory during operation of such
a
computer system. The software components can comprise both software components
that are
standard in the art and components that are special to the present invention
(e.g., dCHIP software
described in Lin et al. (2004) Bioinformatics 20, 1233-1240; CRLMM software
described in
Silver et al. (2007) Cell 128, 991-1002; Aroma Affymetrix software described
in Richardson et
al. (2006) Cancer Cell 9, 121-132. The methods of the invention can also be
programmed or
modeled in mathematical software packages that allow symbolic entry of
equations and high-
level specification of processing, including specific algorithms to be used,
thereby freeing a user
of the need to procedurally program individual equations and algorithms. Such
packages
include, e.g., Matlab from Mathworks (Natick, Mass.), Mathematica from Wolfram
Research
(Champaign, Ill.) or S-Plus from MathSoft (Seattle, Wash.). In certain
embodiments, the
computer comprises a database for storage of hybridization signal profiles.
Such stored profiles
can be accessed and used to calculate a copy number, copy number loss, copy
number gain,
LOH, mutation, deletion and expression level. For example, of the
hybridization signal profile
of a sample derived from the non-cancerous tissue of a subject and/or profiles
generated from
population-based distributions of AKT pathway components and genomic loci in
relevant
populations of the same species were stored, it could then be compared to the
hybridization
signal profile of a sample derived from the cancerous tissue of the subject.
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In addition to the exemplary program structures and computer systems described
herein,
other, alternative program structures and computer systems will be readily
apparent to the skilled
artisan. Such alternative systems, which do not depart from the above
described computer
system and programs structures either in spirit or in scope, are therefore
intended to be
comprehended within the accompanying claims.
Once a laboratory technician or laboratory professional or group of laboratory
technicians
or laboratory professionals determines whether a sample has a copy number,
copy number gain,
copy number loss, or expression level as described above (e.g., step (1) in
many of the methods
above), the same or a different laboratory technician or laboratory
professional (or group) can
analyze a plurality of tests of AKT pathway components and genomic loci to
determine whether
there is a copy number, copy number loss, copy number gain, LOH, mutation, or
deletion to
determine the expression levels (e.g., step (2) in many of the methods above).
Next, the same or
a different laboratory technician or laboratory professional (or group) can
combine copy number,
copy number loss, copy number gain, LOH, mutation, or deletion, or expression
level data from
the test of AKT pathway components and genomic loci to derive a copy number,
copy number
loss, copy number gain, LOH, mutation, or deletion, or expression level (e.g.,
step (3) in many of
the methods above). Optionally, the same or a different laboratory technician
or laboratory
professional (or group) can correlate the copy number, copy number loss, LOH,
mutation, or
deletion, or expression level to an increased or decreased likelihood of
response to a particular
therapy (e.g., those mentioned above).
In various embodiments, provided herein is a computer readable storage medium
comprising: a storing data module containing data from a sample comprising a
cancer cell
obtained from a subject that represents an expression level from an assay for
AKT pathway
components and genomic loci; a comparison module that compares the data stored
on the storing
data module with a reference data and/or control data, and to provide a
comparison content, and
an output module displaying the comparison content for the user, wherein the
expression pattern
of AKT pathway components and genomic loci indicates that the subject is has a
certain AKT
cancer subtype and an appropriate therapy that is likely effective to this AKT
cancer subtype
should be selected or prescribed and administered to the subject as the
subject may not
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adequately respond to other therapies. Also, the subject may be instructed to
take the appropriate
therapy that is likely effective to his or her AKT cancer subtype.
In various embodiments, the control data comprises data from a population of
cancer
patients. In various embodiments, the control data comprises data from a
population of non-
cancerous healthy individuals. In various embodiments, the control data
comprises data from a
housekeeping gene expression.
Embodiments of the invention can be described through functional modules,
which are
defined by computer executable instructions recorded on computer readable
media and which
cause a computer to perform method steps when executed. The modules are
segregated by
a)
function, for the sake of clarity. However, it should be understood that the
modules/systems
need not correspond to discreet blocks of code and the described functions can
be carried out by
the execution of various code portions stored on various media and executed at
various times.
Furthermore, it should be appreciated that the modules may perform other
functions, thus the
modules are not limited to having any particular functions or set of
functions.
The computer readable storage media can be any available tangible media that
can be
accessed by a computer. Computer readable storage media includes volatile and
nonvolatile,
removable and non-removable tangible media implemented in any method or
technology for
storage of information such as computer readable instructions, data
structures, program modules
or other data. Computer readable storage media includes, but is not limited
to, RAM (random
access memory), ROM (read only memory), EPROM (erasable programmable read only
memory), EEPROM (electrically erasable programmable read only memory), flash
memory or
other memory technology, CD-ROM (compact disc read only memory), DVDs (digital
versatile
disks), BLU-RAY disc or other optical storage media, magnetic cassettes,
magnetic tape,
magnetic disk storage or other magnetic storage media, other types of volatile
and non-volatile
memory, and any other tangible medium which can be used to store the desired
information and
which can accessed by a computer including and any suitable combination of the
foregoing.
Computer-readable data embodied on one or more computer-readable media may
define
instructions, for example, as part of one or more programs that, as a result
of being executed by a
computer, instruct the computer to perform one or more of the functions
described herein, and/or
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various embodiments, variations and combinations thereof. Such instructions
may be written in
any of a plurality of programming languages, for example, Java, J#, Visual
Basic, C, C#, C++,
Fortran, Pascal, Eiffel, Basic, COBOL assembly language, and the like, or any
of a variety of
combinations thereof. The computer-readable media on which such instructions
are embodied
may reside on one or more of the components of either of a system, or a
computer readable
storage medium described herein, may be distributed across one or more of such
components.
The computer-readable media may be transportable such that the instructions
stored
thereon can be loaded onto any computer resource to implement the aspects of
the present
invention discussed herein. In addition, it should be appreciated that the
instructions stored on
the computer-readable medium, described above, are not limited to instructions
embodied as part
of an application program running on a host computer. Rather, the instructions
may be
embodied as any type of computer code (e.g., software or microcode) that can
be employed to
program a computer to implement aspects of the present invention. The computer
executable
instructions may be written in a suitable computer language or combination of
several languages.
Basic computational biology methods are known to those of ordinary skill in
the art and are
described in, for example, Setubal and Meidanis et al., Introduction to
Computational Biology
Methods (PWS Publishing Company, Boston, 1997);
Salzberg, Searles, Kasif, (Ed.),
Computational Methods in Molecular Biology, (Elsevier, Amsterdam, 1998);
Rashidi and
Buehler, Bioinformatics Basics: Application in Biological Science and Medicine
(CRC Press,
London, 2000) and Ouelette and Bzevanis Bioinformatics: A Practical Guide for
Analysis of
Gene and Proteins (Wiley & Sons, Inc., 2nd ed., 2001).
The functional modules of certain embodiments of the invention include for
example, at a
measuring module, a storage module, a comparison module, and an output module.
The
functional modules can be executed on one, or multiple, computers, or by using
one, or multiple,
computer networks. The measuring module has computer executable instructions
to provide e.g.,
expression information in non-transitory computer readable form.
The measuring module can comprise any system for detecting the expression
patterns of
AKT pathway components and status of genetic loci (e.g., copy number
alterations, copy number
gain or loss, LOH, mutations, amplifications and deletions). Such systems can
include DNA
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microarrays, RNA expression arrays, any ELISA detection system and/or any
Western blotting
detection system.
The information determined in the determination system can be read by the
storage
module. As used herein the "storage module" is intended to include any
suitable computing or
processing apparatus or other device configured or adapted for storing data or
information.
Examples of electronic apparatus suitable for use with the present invention
include stand-alone
computing apparatus, data telecommunications networks, including local area
networks (LAN),
wide area networks (WAN), Internet, Intranet, and Extranet, and local and
distributed computer
processing systems. Storage modules also include, but are not limited to:
magnetic storage
media, such as floppy discs, hard disc storage media, magnetic tape, optical
storage media such
as CD-ROM, DVD, electronic storage media such as RAM, ROM, EPROM, EEPROM and
the
like, general hard disks and hybrids of these categories such as
magnetic/optical storage media.
The storage module is adapted or configured for having recorded thereon
expression level or
protein level information. Such information may be provided in digital form
that can be
transmitted and read electronically, e.g., via the Internet, on diskette, via
USB (universal serial
bus) or via any other suitable mode of communication.
As used herein, "stored" refers to a process for encoding information on the
storage
module. Those skilled in the art can readily adopt any of the presently known
methods for
recording information on known media to generate manufactures comprising
expression level
information.
In one embodiment the reference data stored in the storage module to be read
by the
comparison module is, for example, expression data obtained from a population
of non-cancer
subjects, a population of cancer subjects, or expression data obtained from
the same subject at a
prior time point using the measuring module.
The "comparison module" can use a variety of available software programs and
formats
for the comparison operative to compare expression data determined in the
measuring module to
reference samples and/or stored reference data. In one embodiment, the
comparison module is
configured to use pattern recognition techniques to compare information from
one or more
entries to one or more reference data patterns. The comparison module may be
configured using
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existing commercially-available or freely-available software for comparing
patterns, and may be
optimized for particular data comparisons that are conducted. The comparison
module provides
computer readable information related to the expression patterns of AKT
pathway components
and status of genetic loci (e.g., copy number alterations, copy number gain or
loss, LOH,
mutations, amplifications and deletions) in an individual, efficacy of
treatment in an individual,
and/or method for treating an individual.
The comparison module, or any other module of the invention, may include an
operating
system (e.g., UNIX) on which runs a relational database management system, a
World Wide
Web application, and a World Wide Web server. World Wide Web application
includes the
executable code necessary for generation of database language statements
(e.g., Structured Query
Language (SQL) statements). Generally, the executables will include embedded
SQL statements.
In addition, the World Wide Web application may include a configuration file
which contains
pointers and addresses to the various software entities that comprise the
server as well as the
various external and internal databases which must be accessed to service user
requests. The
Configuration file also directs requests for server resources to the
appropriate hardware--as may
be necessary should the server be distributed over two or more separate
computers. In one
embodiment, the World Wide Web server supports a TCP/IP protocol. Local
networks such as
this are sometimes referred to as "Intranets. An advantage of such Intranets
is that they allow
easy communication with public domain databases residing on the World Wide Web
(e.g., the
GenBank or Swiss Pro World Wide Web site). Thus, in a particular preferred
embodiment of the
present invention, users can directly access data (via Hypertext links for
example) residing on
Internet databases using a HTML interface provided by Web browsers and Web
servers.
The comparison module provides a computer readable comparison result that can
be
processed in computer readable form by predefined criteria, or criteria
defined by a user, to
provide a content-based in part on the comparison result that may be stored
and output as
requested by a user using an output module.
The content based on the comparison result, may be an expression value
compared to a
reference showing the susceptibility/adequate response or
nonsusceptibility/non-adequate
response from standard, conventional or certain therapy.
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In various embodiments of the invention, the content based on the comparison
result is
displayed on a computer monitor. In various embodiments of the invention, the
content based on
the comparison result is displayed through printable media. The display module
can be any
suitable device configured to receive from a computer and display computer
readable
information to a user. Non-limiting examples include, for example, general-
purpose computers
such as those based on Intel PENTIUM-type processor, Motorola PowerPC, Sun
UltraSPARC,
Hewlett-Packard PA-RISC processors, any of a variety of processors available
from Advanced
Micro Devices (AMD) of Sunnyvale, California, or any other type of processor,
visual display
devices such as flat panel displays, cathode ray tubes and the like, as well
as computer printers of
various types.
In one embodiment, a World Wide Web browser is used for providing a user
interface for
display of the content based on the comparison result. It should be understood
that other
modules of the invention can be adapted to have a web browser interface.
Through the Web
browser, a user may construct requests for retrieving data from the comparison
module. Thus,
the user will typically point and click to user interface elements such as
buttons, pull down
menus, scroll bars and the like conventionally employed in graphical user
interfaces.
The present invention therefore provides for systems (and computer readable
media for
causing computer systems) to perform methods for selecting treatment of cancer
in an individual.
As used herein, "selecting treatment" refers to selecting, choosing or
prescribing a cancer
treatment for the individual, or instructing or directing the individual to
receive a cancer
treatment.
Systems and computer readable media described herein are merely illustrative
embodiments of the invention for detecting the expression patterns of AKT
pathway components
and status of genetic loci (e.g., copy number alterations, copy number gain or
loss, LOH,
mutations, amplifications and deletions) in an individual, and are not
intended to limit the scope
of the invention. Variations of the systems and computer readable media
described herein are
possible and are intended to fall within the scope of the invention.
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The modules of the machine, or those used in the computer readable medium, may
assume numerous configurations. For example, function may be provided on a
single machine
or distributed over multiple machines.
In some cases, a computing system provided herein can include computer-
executable
instructions or a computer program (e.g., software) containing computer-
executable instructions
for formatting an output providing an indication the expression patterns of
AKT pathway
components and status of genetic loci (e.g., copy number alterations, copy
number gain or loss,
LOH, mutations, amplifications and deletions) or a likelihood that a cancer
patient will respond
to a particular cancer treatment regimen (e.g., a regimen as described above),
or a combination of
these items. In some cases, a computing system provided herein can include
computer-
executable instructions or a computer program (e.g., software) containing
computer-executable
instructions for determining a desired cancer treatment regimen for a
particular patient based at
least in part on the expression patterns of AKT pathway components and status
of genetic loci
(e.g., copy number alterations, copy number gain or loss, LOH, mutations,
amplifications and
deletions).
In some cases, a computing system provided herein can include a pre-processing
device
configured to process a sample (e.g., cancer cells) such that a SNP array-
based assay or
sequencing-based assay can be performed. Examples of pre-processing devices
include, without
limitation, devices configured to enrich cell populations for cancer cells as
opposed to non-
cancer cells, devices configured to lyse cells and/or extract genomic nucleic
acid, and devices
configured to enrich a sample for particular genomic DNA fragments.
Expression Pattern Assay ¨ RNA
In various embodiments, determining an expression pattern of AKT pathway
components
in the biological sample comprises assaying mRNA levels. In various
embodiments, assaying
mRNA levels comprises using RNA sequencing, northern blot, in situ
hybridization,
hybridization array, serial analysis of gene expression (SAGE), reverse
transcription PCR, real-
time PCR, real-time reverse transcription PCR, quantitative PCR, or
microarray, or a
combination thereof.
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In various embodiments, assaying mRNA levels comprises contacting the
biological
sample with polynucleotide probes capable of specifically hybridizing to mRNA
of one or more
AKT pathway components and thereby forming probe-target hybridization
complexes.
Hybridization-based RNA assays include, but are not limited to, traditional
"direct probe"
methods such as, northern blot or in situ hybridization (e.g., Angerer (1987)
Meth. Enzymol 152:
649). The methods can be used in a wide variety of formats including, but not
limited to,
substrate (e.g. membrane or glass) bound methods or array-based approaches. In
a typical in situ
hybridization assay, cells are fixed to a solid support, typically a glass
slide. If a nucleic acid is
to be probed, the cells are typically denatured with heat or alkali. The cells
are then contacted
with a hybridization solution at a moderate temperature to permit annealing of
labeled probes
specific to the nucleic acid sequence encoding the protein. The targets (e.g.,
cells) are then
typically washed at a predetermined stringency or at an increasing stringency
until an appropriate
signal to noise ratio is obtained. The probes are typically labeled, e.g.,
with radioisotopes or
fluorescent reporters. Preferred probes are sufficiently long so as to
specifically hybridize with
the target nucleic acid(s) under stringent conditions. The preferred size
range is from about 200
bases to about 1000 bases. Hybridization protocols suitable for use with the
methods of the
invention are described, e.g., in Albertson (1984) EMBO J. 3: 1227-1234;
Pinkel (1988) Proc.
Natl. Acad. Sci. USA 85: 9138-9142; EPO Pub. No. 430,402; Methods in Molecular
Biology,
Vol. 33: In situ Hybridization Protocols, Choo, ed., Humana Press, Totowa,
N.J. (1994), Pinkel,
et al. (1998) Nature Genetics 20: 207-211, and/or Kallioniemi (1992) Proc.
Natl Acad Sci USA
89:5321-5325 (1992). In some applications, it is necessary to block the
hybridization capacity of
repetitive sequences. Thus, in some embodiments, tRNA, human genomic DNA, or
Cot-I DNA
is used to block non-specific hybridization.
In various embodiments, assaying mRNA levels comprises contacting the
biological
sample with polynucleotide primers capable of specifically hybridizing to
mRNAs of genes
listed in Table 2, forming primer-template hybridization complexes, and
performing a PCR
reaction. In some embodiments, the polynucleotide primers comprises about 15-
45, 20-40, or
25-35 bp sequences that are identical (for forward primers) or complementary
(for reverse
primers) to sequences of genes listed in Table 2. As a non-liming example, the
polynucleotide
primers for ACLY (e.g., transcript variant 1 NM 001096.2 with 4450 bp) can
comprise
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sequences that are identical (for forward primers) or complementary (for
reverse primers) to
ACLY's bp 1-20, 5-25, 10-30, 15-35, 20-40, 25-45, 30-50, so on and so forth,
until the end of
ACLY, 4410-4430, 4415-4435, 4420-4440, 4425-4445, 4430-4450. While not listed
here
exhaustively because of the space, all these polynucleotide primers for ACLY
and other genes
listed in Table 2 can be used in the present invention. In various
embodiments, the
polynucleotide primers are labeled with radioisotopes or fluorescent
molecules. As the labeled
primers emit radio or fluorescent signals, the PCR products containing the
labeled primers can be
detected and analyzed with a variety of imaging equipment.
Methods of "quantitative" amplification are well known to those of skill in
the art. For
example, quantitative PCR involves simultaneously co-amplifying a known
quantity of a control
sequence using the same primers. This provides an internal standard that may
be used to
calibrate the PCR reaction. Detailed protocols for quantitative PCR are
provided in Innis, et al.
(1990) PCR Protocols, A Guide to Methods and Applications, Academic Press,
Inc. N.Y.).
Measurement of DNA copy number at microsatellite loci using quantitative PCR
anlaysis is
described in Ginzonger, et al. (2000) Cancer Research 60:5405-5409. The known
nucleic acid
sequence for the genes is sufficient to enable one of skill in the art to
routinely select primers to
amplify any portion of the gene. Fluorogenic quantitative PCR may also be used
in the methods
of the invention. In fluorogenic quantitative PCR, quantitation is based on
amount of
fluorescence signals, e.g., TaqMan and sybr green. Other suitable
amplification methods
include, but are not limited to, ligase chain reaction (LCR) (see Wu and
Wallace (1989)
Genomics 4: 560, Landegren, et al. (1988) Science 241:1077, and Barringer et
al. (1990) Gene
89: 117), transcription amplification (Kwoh, et al. (1989) Proc. Natl. Acad.
Sci. USA 86: 1173),
self-sustained sequence replication (Guatelli, et al. (1990) Proc. Nat. Acad.
Sci. USA 87: 1874),
dot PCR, and linker adapter PCR, etc.
Expression Level Assay ¨ Protein
In various embodiments, determining an expression pattern of AKT pathway
components
in the biological sample comprises assaying protein levels. In various
embodiments, assaying a
protein level comprises using western blot, enzyme-linked immunosorbent assay
(ELISA),
radioimmunoassay, or mass spectrometry, or a combination thereof.
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In various embodiments, assaying protein levels comprises contacting the
biological
sample with antibodies capable of specifically binding to proteins encoded by
genes listed in
Table 2 and thereby forming antigen-antibody complexes. In the methods and
assays of the
invention, the expression levels of proteins encoded by genes listed in Table
2, or fragments or
variants thereof can be determined using antibodies specific for those
individual proteins or
fragments or variants thereof and detecting immunospecific binding of each
antibody to its
respective cognate biomarker protein.
Antibodies, both polyclonal and monoclonal, can be produced by a skilled
artisan either
by themselves using well known methods or they can be manufactured by service
providers who
specialize making antibodies based on known protein sequences. In the present
invention, the
protein sequences of AKT pathway genes are known and thus production of
antibodies against
them is a matter of routine.
For example, production of monoclonal antibodies can be performed using the
traditional
hybridoma method by first immunizing mice with an antigen which may be an
isolated protein of
choice or fragment thereof (for example, a protein encode by a gene listed in
Table 2, or a
fragment thereof or a variant thereof) and making hybridoma cell lines that
each produce a
specific monoclonal antibody. The antibodies secreted by the different clones
are then assayed
for their ability to bind to the antigen using, e.g., ELISA or Antigen
Microarray Assay, or
immuno-dot blot techniques. The antibodies that are most specific for the
detection of the
protein of interest can be selected using routine methods and using the
antigen used for
immunization and other antigens as controls. The antibody that most
specifically detects the
desired antigen and protein and no other antigens or proteins are selected for
the processes,
assays and methods described herein. The best clones can then be grown
indefinitely in a
suitable cell culture medium. They can also be injected into mice (in the
peritoneal cavity,
surrounding the gut) where they produce an antibody-rich ascites fluid from
which the antibodies
can be isolated and purified. The antibodies can be purified using techniques
that are well
known to one of ordinary skill in the art.
Any suitable immunoassay method may be utilized, including those which are
commercially available, to determine the expression level of an AKT pathway
protein or a
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variant thereof assayed according to the invention. Extensive discussion of
the known
immunoassay techniques is not required here since these are known to those of
skill in the art.
Typical suitable immunoassay techniques include sandwich enzyme-linked
immunoassays
(ELISA), radioimmunoassays (RIA), competitive binding assays, homogeneous
assays,
heterogeneous assays, etc.
For example, in the assays of the invention, "sandwich-type" assay formats can
be used.
An alternative technique is the "competitive-type" assay. In a competitive
assay, the labeled
probe is generally conjugated with a molecule that is identical to, or an
analog of, the analyte.
Thus, the labeled probe competes with the analyte of interest for the
available receptive material.
to Competitive assays are typically used for detection of analytes such as
haptens, each hapten
being monovalent and capable of binding only one antibody molecule.
The antibodies can be labeled. In some embodiments, the detection antibody is
labeled
by covalently linking to an enzyme, label with a fluorescent compound or
metal, label with a
chemiluminescent compound. For example, the detection antibody can be labeled
with catalase
and the conversion uses a colorimetric substrate composition comprises
potassium iodide,
hydrogen peroxide and sodium thiosulphate; the enzyme can be alcohol
dehydrogenase and the
conversion uses a colorimetric substrate composition comprises an alcohol, a
pH indicator and a
pH buffer, wherein the pH indicator is neutral red and the pH buffer is
glycine-sodium
hydroxide; the enzyme can also be hypoxanthine oxidase and the conversion uses
a colorimetric
substrate composition comprises xanthine, a tetrazolium salt and 4,5-dihydroxy-
1,3-benzene
disulphonic acid. In one embodiment, the detection antibody is labeled by
covalently linking to
an enzyme, label with a fluorescent compound or metal, or label with a
chemiluminescent
compound.
Direct and indirect labels can be used in immunoassays. A direct label can be
defined as
an entity, which in its natural state, is visible either to the naked eye or
with the aid of an optical
filter and/or applied stimulation, e.g., ultraviolet light, to promote
fluorescence. Examples of
colored labels which can be used include metallic sol particles, gold sol
particles, dye sol
particles, dyed latex particles or dyes encapsulated in liposomes. Other
direct labels include
radionuclides and fluorescent or luminescent moieties. Indirect labels such as
enzymes can also
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be used according to the invention. Various enzymes are known for use as
labels such as, for
example, alkaline phosphatase, horseradish peroxidase, lysozyme, glucose-6-
phosphate
dehydrogenase, lactate dehydrogenase and urease.
The antibody can be attached to a surface. Examples of useful surfaces on
which the
antibody can be attached for the purposes of detecting the desired antigen
include nitrocellulose,
PVDF, polystyrene, and nylon.
In some embodiments of the processes, assays and methods described herein,
detecting
the level of antibodies reactive to an AKT pathway protein or a variant
thereof includes
contacting the sample from the cancer patient with an antibody or a fragment
thereof that
specifically binds an AKT pathway protein or a variant thereof, forming an
antibody-protein
complex between the antibody and the AKT pathway protein or the variant
thereof present in the
sample, washing the sample to remove the unbound antibody, adding a detection
antibody that is
labeled and is reactive to the antibody bound to the AKT pathway protein or a
variant thereof in
the sample, washing to remove the unbound labeled detection antibody and
converting the label
to a detectable signal, wherein the detectable signal is indicative of the
level of AKT pathway
protein or a variant thereof in the sample from the patient. In some
embodiments, the effector
component is a detectable moiety selected from the group consisting of a
fluorescent label, a
radioactive compound, an enzyme, a substrate, an epitope tag, electron-dense
reagent, biotin,
digonigenin, hapten and a combination thereof. In some embodiments, the
detection antibody is
labeled by covalently linking to an enzyme, labeled with a fluorescent
compound or metal,
labeled with a chemiluminescent compound. The level of AKT pathway protein may
be
obtained by assaying a light scattering intensity resulting from the formation
of an antibody-
protein complex formed by a reaction of AKT pathway protein in the sample with
the antibody,
wherein the light scattering intensity of at least 10% above a control light
scattering intensity
indicates the likelihood of chemotherapy resistance.
Reference Value of Expression Level
Various methods described herein may compare an AKT pathway gene's expression
level in a subject's biological sample to a pre-determined reference value of
the AKT pathway
gene. In various embodiments, an AKT pathway gene's reference value of
expression level is
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the AKT pathway gene's median or mean expression level from all tumor samples
in the
discovery dataset. In various embodiments, an AKT pathway gene's reference
value of
expression level is the AKT pathway gene's median or mean expression level
from all GBM
samples in the discovery dataset. In various embodiments, an AKT pathway
gene's reference
value of expression level is the AKT pathway gene's median or mean expression
level from all
tumor samples in the validation dataset. In various embodiments, an AKT
pathway gene's
reference value of expression level is the AKT pathway gene's median or mean
expression level
from all GBM samples in the validation dataset. In various embodiments, an AKT
pathway
gene's reference value of expression level is the AKT pathway gene's median or
mean
expression level from non-cancerous, non-tumorous, or non-neoplastic cells or
tissues. In
accordance with the present invention, AKT pathway genes include but are not
limited to those
listed in Table 2.
Reference values may be obtained by various methods known in the field. For
example,
one or more biopsies from one cancer patient' tumor (hereinafter "Tumor-1")
may be collected,
processed and analyzed to obtain the expression level of one AKT pathway gene
(hereinafter
"Gene-1") in this tumor (hereinafter "Expression-Tumor-l-Gene-1"). The same
step is used to
obtain Gene-i's expression levels in another 10, 100, 200, 300, 400, 500, 600,
700, 800, 900,
1000 or more cancer patients' tumors (hereinafter "Tumor-N), that is,
"Expression-Tumor-N-
Gene-1" (N is 1, 2, 3, 4, 5, 6, 7, ...). Then, Gene-l's median or mean
expression level from all
tumors may be used as the reference value of Gene-1 (hereinafter "REF-Gene-
1"), to which
Gene-l's expression in a subject's biological sample is compared to so as to
determine if Gene-
l's expression is high or low in the subject's biological sample. In other
words, REF-Gene-1 is
the median or mean of Expression-Tumor-N-Gene-1. Similar steps may be used to
obtain
another 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90,
95, 100, or more AKT
pathway genes' reference values, that is, "REF-Gene-M" (M=1, 2, 3, 4, 5, 6, 7,
...). In various
embodiments, non-limiting AKT pathway genes (i.e., Gene-M) are listed in Table
2. To
determine the expression pattern of AKT pathway genes in a subject's
biological sample, one
may compare one, two, three, four, five, or more AKT pathway genes' expression
levels to their
respective reference values.
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As used herein, "expression pattern", "expression profile" and "expression
signature" are
exchangeable terms referring to the specific combination or setting of one or
more genes' high
(increased) expressions and/or low (decreased) expressions relative to
reference values. In
various embodiments, AKT cancer subtypes' expression patterns are the specific
combinations
of AKT pathway genes' high and low expressions. For non-limiting example,
Figure 10 shows
the expression patterns of AKT MES, CLAS, PROLIF, SL and SN subtypes in the
validation and
discovery datasets. Among the 64 exemplar AKT pathway genes shown in Figure
10, those
having high expressions relative to reference values are shown as red, and
those having low
expressions relative to reference values are shown as green.
Various statistical methods, for example, a two-tailed student t-test with
unequal
variation, may be used to measure the differences in expression levels of an
AKT pathway gene
between the subject's sample and a reference value of expression level
generate by computer
algorithm pooling many tumor samples, as described herein, for example, all
the GBM samples
in the discovery dataset and/or validation dataset. Various statistical
methods, for example, a
two-tailed student t-test with unequal variation, may be used to measure the
differences in
expression levels of an AKT pathway gene between the subject's sample and a
control sample
from a normal/healthy individual. Various statistical methods, for example, a
two-tailed student
t-test with unequal variation, may be used to measure the differences in
expression levels of an
AKT pathway gene between the subject's sample and a reference value of
expression level
generate by computer algorithm pooling many control samples, as described
herein. A
significant difference may be achieved where the p value is equal to or less
than 0.05.
In various embodiments, the expression level of an AKT pathway gene or a
variant
thereof in the subject as compared to the reference value is higher by at
least or about 5, 10, 15,
20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100%. In
various embodiments,
the expression level of an AKT pathway gene or a variant thereof in the
subject as compared to
the reference value is lower by at least or about 5, 10, 15, 20, 25, 30, 35,
40, 45, 50, 55, 60, 65,
70, 75, 80, 85, 90, 95, or 100%. In various embodiments, the expression level
ratio between an
AKT pathway gene or a variant thereof in the subject and the reference value
is at least or about
1.1:1, 1.2:1, 1.3:1, 1.4:1, 1.5:1, 1.6:1, 1.7:1, 1.8:1, 1.9:1, 2:1, 2.1:1,
2.2:1, 2.3:1, 2.4:1, 2.5:1,
2.6:1, 2.7:1, 2.8:1, 2.9:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1 or 10:1, 15:1,
20:1, 25:1, 30:1, 35:1,
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40:1,45:1, 50:1, 55:1, 60:1, 65:1, 70:1, 75:1, 80:1, 85:1, 90:1, 95:1, or
100:1. In various
embodiments, the expression level ratio between the reference value and an AKT
pathway gene
or a variant thereof in the subject is at least or about 1.1:1, 1.2:1, 1.3:1,
1.4:1, 1.5:1, 1.6:1, 1.7:1,
1.8:1, 1.9:1, 2:1, 2.1:1, 2.2:1, 2.3:1, 2.4:1, 2.5:1, 2.6:1, 2.7:1, 2.8:1,
2.9:1, 3:1, 4:1, 5:1, 6:1, 7:1,
8:1, 9:1 or 10:1, 15:1, 20:1, 25:1, 30:1, 35:1, 40:1, 45:1, 50:1, 55:1, 60:1,
65:1, 70:1, 75:1, 80:1,
85:1, 90:1, 95:1, or 100:1.
Many variations and alternative elements have been disclosed in embodiments of
the
present invention. Still further variations and alternate elements will be
apparent to one of skill
in the art. Among these variations, without limitation, are the selection of
constituent modules
for the inventive compositions, and the diseases and other clinical conditions
that may be
diagnosed, prognosed or treated therewith. Various embodiments of the
invention can
specifically include or exclude any of these variations or elements.
In some embodiments, the numbers expressing quantities of ingredients,
properties such
as concentration, reaction conditions, and so forth, used to describe and
claim certain
embodiments of the invention are to be understood as being modified in some
instances by the
term "about." Accordingly, in some embodiments, the numerical parameters set
forth in the
written description and attached claims are approximations that can vary
depending upon the
desired properties sought to be obtained by a particular embodiment. In some
embodiments, the
numerical parameters should be construed in light of the number of reported
significant digits
and by applying ordinary rounding techniques. Notwithstanding that the
numerical ranges and
parameters setting forth the broad scope of some embodiments of the invention
are
approximations, the numerical values set forth in the specific examples are
reported as precisely
as practicable. The numerical values presented in some embodiments of the
invention may
contain certain errors necessarily resulting from the standard deviation found
in their respective
testing measurements.
Groupings of alternative elements or embodiments of the invention disclosed
herein are
not to be construed as limitations. Each group member can be referred to and
claimed
individually or in any combination with other members of the group or other
elements found
herein. One or more members of a group can be included in, or deleted from, a
group for reasons
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of convenience and/or patentability. When any such inclusion or deletion
occurs, the
specification is herein deemed to contain the group as modified thus
fulfilling the written
description of all Markush groups used in the appended claims.
EXAMPLES
The invention will be further explained by the following Examples, which are
intended to
be purely exemplary of the invention, and should not be considered as limiting
the invention in
any way. The following examples are provided to better illustrate the claimed
invention and are
not to be interpreted as limiting the scope of the invention. To the extent
that specific materials
are mentioned, it is merely for purposes of illustration and is not intended
to limit the invention.
One skilled in the art may develop equivalent means or reactants without the
exercise of
inventive capacity and without departing from the scope of the invention.
Example 1: Materials and Methods
Patient Information
The discovery dataset (GBM195) consisted of 181 GBM (WHO grade IV astrocytoma;
(159 primary and 22 recurrent) from 3 datasets [3], [4], [21] and 14 non-
neoplastic samples from
2 sources: (1) six samples from patients undergoing temporal lobe epilepsy
surgery [3] and (2)
eight samples from autopsy specimens of cerebral cortex from donors with no
history of
neurological disorders obtained from the National Neurological Research Brain
Bank (Los
Angeles, CA) [4]. Two datasets are in GEO (GSE4271, GSE4412) and the third has
been
submitted. Table 1 lists GEO ID's and clinical information for GBM195 tumors.
Tissue
collection and processing, pathological review, and microarray analysis for
the discovery dataset
(GBM195) has been described elsewhere ([3] Nigro et al. 2005, [4] Phillips et
a. 2006, and [21]
Freije et al. 2004, which are incorporated herein by reference in their
entirety as though fully set
forth.) The validation dataset consisted of 583 samples; 573 GBM (16 recurrent
and 3
secondary) and 10 non-neoplastic samples from The Cancer Genome Atlas (TCGA).
Samples
were collected and processed as described ([5] Atlas TCG 2008, which is
incorporated herein by
reference in its entirety as though fully set forth.). IRB or Committee on
Human Research
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approval was obtained for samples used in the discovery and validation
datasets as described [3],
[4], [10], [21].
49
Table 1: Clinical information for tumors in GBM195
GEO_Accessions
Phillips Survival Censoring 0
id (U133A/U133B) Institution Histology
Anat. Site Recurrence Subclass Gender Age Weeks
Status n.)
o
1¨,
G1022 GSM99544,GSM99545 UCLA GBM Mes
male 31 18 D vi
G1028 GSM99465,GSM99464 UCLA GBM
Unk female 20 7.7 D --4
--4
--4
G1032 GSM99483,GSM99482 UCLA GBM
PN female 34 12.9 D n.)
vi
G1038 GSM99581,GSM99580 UCLA GBM PN
female 33 178.1 A
G1043 GSM99560,GSM99561 UCLA GBM Mes
female 23 155.6 D
G1334 GSM99529,GSM99528 UCLA GBM
PN female 36 43.1 D
G1342 GSM99471,GSM99470 UCLA GBM PN
male 54 32 D
G1354 GSM99551,GSM99550 UCLA GBM Mes
male 42 60 D
G1398 GSM99491,GSM99490 UCLA GBM
Mes female 49 41.9 D
G1406 GSM99543,GSM99542 UCLA GBM Mes
male 29 33.7 D P
r.,
G1414 GSM99466,GSM99467 UCLA GBM
Mes female 69 9.1 D .
r.,
vi G1423 GSM99493,GSM99492 UCLA
GBM PN female 54 13.7 D ,
o r.,
G1463 GSM99475,GSM99474 UCLA GBM PN
male 30 37.9 D
,
,
G1469 GSM99494,GSM99495 UCLA GBM Mes
male 56 21.9 D .
,
G1478 GSM99553,GSM99552 UCLA GBM PN
male 40 155.4 A .
,
G1495 GSM99457,GSM99456 UCLA GBM
PN female 82 10.1 D
G1511 GSM99451,GSM99450 UCLA GBM PN
male 27 12.1 D
G1516 GSM99555,GSM99554 UCLA GBM Mes
female 41 147.3 A
G1521 GSM99563,GSM99562 UCLA GBM PN
female 23 146 A
G1544 GSM99488,GSM99489 UCLA GBM
Mes female 49 21.1 D
Iv
G1656 GSM99440,GSM99441 UCLA GBM PN
male 48 137.3 A n
G1667 GSM99447,GSM99446 UCLA GBM Mes
male 44 84 D
cp
G1675 GSM99565,GSM99564 UCLA GBM Mes
male 61 97.6 D n.)
o
1¨,
G1681 GSM99589,GSM99588 UCLA GBM Mes
male 40 132.4 A .6.
G1745 GSM99448,GSM99449 UCLA GBM PN
female 42 111.4 A c:
--4
1¨,
G1798 GSM99556,GSM99557 UCLA GBM Mes
female 47 103.3 A c:
oe
GEO_Accessions
Phillips Survival Censoring
id (U133A/U133B) Institution Histology
Anat. Site Recurrence Subclass Gender Age Weeks
Status
0
G1900 GSM99485,GSM99484 UCLA GBM
Prolif female 45 39.9 D n.)
o
G1902 GSM99442,GSM99443 UCLA GBM
Mes female 56 46.4 D
vi
G1905 GSM99583,GSM99582 UCLA GBM
PN male 75 55.6 D -,-:--,
-4
-4
G2013 GSM99591,GSM99590 UCLA GBM
Mes female 70 56.6 A --4
n.)
vi
G2015 GSM99445,GSM99444 UCLA GBM
Mes male 78 56.6 A
G2017 GSM99578,GSM99579 UCLA GBM
Mes male 60 33.9 D
G2028 GSM99531,GSM99530 UCLA GBM
PN female 42 31.9 D
G2029 GSM99533,GSM99532 UCLA GBM
PN female 42 31.9 D
G2067 GSM99538,GSM99539 UCLA GBM
PN female 42 24 D
G2068 GSM99540,GSM99541 UCLA GBM
PN female 42 24 D
G2079 GSM99486,GSM99487 UCLA GBM
Mes male 64 42.6 A p
G2098 GSM99585,GSM99584 UCLA GBM
Mes male 65 29 A "
r.,
vi G2158 GSM99472,GSM99473 UCLA GBM
PN female 62 13.6 D .
,
1-,
r.,
G2166 GSM99559,GSM99558 UCLA GBM
PN female 39 156.9 A "
,
'
G585 GSM99587,GSM99586 UCLA GBM
PN female 63 43.1 D .
,
G597 GSM99534,GSM99535 UCLA GBM
Mes male 35 1 D
,
G604 GSM99572,GSM99573 UCLA GBM
Mes male 66 26.4 D
G636 GSM99476,GSM99477 UCLA GBM
Prolif female 54 58.9 D
G660 GSM99546,GSM99547 UCLA GBM
PN female 75 16 D
G697 GSM99436,GSM99437 UCLA GBM
Mes female 64 50.9 D
G706 GSM99453,GSM99452 UCLA GBM
PN male 54 72.3 D
G712 GSM99432,GSM99433 UCLA GBM
Mes male 49 26.9 D Iv
n
G746 GSM99525,GSM99524 UCLA GBM
PN male 52 6.1 D 1-3
G749 GSM99462,GSM99463 UCLA GBM
Mes male 39 7.6 D cp
n.)
o
G782 GSM99577,GSM99576 UCLA GBM
PN female 24 20 D
.6.
-,-:--,
G824 GSM99478,GSM99479 UCLA GBM
PN female 50 26.6 D c:
--4
1-,
G839 GSM99481,GSM99480 UCLA GBM
PN male 82 40.9 D c:
oe
G931 GSM99438,GSM99439 UCLA GBM
Mes female 58 26 D
GEO_Accessions
Phillips Survival Censoring
id (U133A/U133B) Institution Histology
Anat. Site Recurrence Subclass Gender Age Weeks
Status
0
G932 GSM99435,GSM99434 UCLA GBM
PN female 18 14 D n.)
o
G938 GSM99536,GSM99537 UCLA GBM
PN male 29 81.3 D
vi
-,-:--,
G976 GSM99548,GSM99549 UCLA GBM
Mes female 43 59.7 D --4
--4
G985 GSM99454,GSM99455 UCLA GBM
PN female 76 8 D --4
n.)
vi
G996 GSM99527,GSM99526 UCLA GBM
Prolif male 45 32 D
MDA10
334 GSM97053,GSM96953 MDA GBM
0 PN male 38 210 A
MDA11
300 GSM97002,GSM97102 MDA GBM
0 Prolif female 68 91 D
MDA11
53 S MDA GBM
1 Unk male 12
MDA13
p
51 GSM96999,GSM97099 MDA GBM
1 Mes male 57 2
r.,
MDA13
n.) 818 S MDA GBM
0 Unk female 8 481 A "
r.,
MDA13
0
,
,
921 GSM96979,GSM97079 MDA GBM
0 Prolif female 60 32 D 0
,
MDA13
2
945 G5M96955,G5M97055 MDA GBM
0 PN male 49 34 D
MDA14
085 G5M97089,G5M96989 MDA GBM
0 Mes male 49 106 D
MDA14
206 G5M97103,G5M97003 MDA GBM
1 Prolif female 68
MDA14
523 G5M97007,G5M97107 MDA GBM
0 Prolif female 30 41 D Iv
n
MDA14
1-3
558 G5M97073,G5M96973 MDA GBM
0 Prolif male 76 52 D cp
n.)
MDA15
1-,
.6.
824 G5M97075,G5M96975 MDA GBM
1 Mes male 43 -,-:--,
c,
MDA16
--4
1-,
713 G5M96960,G5M97060 MDA GBM
1 Mes female 43 c:
oe
GEO_Accessions
Phillips Survival Censoring
id (U133A/U133B) Institution Histology
Anat. Site Recurrence Subclass Gender Age Weeks
Status
MDA16
0
n.)
789 GSM96987,GSM97087 MDA GBM
0 Mes male 34 33 D
1-,
vi
MDA17
-,-:--,
-4
467 GSM97005,GSM97105 MDA GBM
1 Mes male 72 --4
--4
MDA17
n.)
vi
65 GSM96952,GSM97052 MDA GBM
0 Mes male 43 313 D
MDA18
395 S MDA GBM
0 Unk male 12 170 A
MDA20
194 S MDA GBM
0 Unk female 55.7 158 D
MDA20
7 GSM97097,GSM96997 MDA GBM
0 Prolif female 32 51 D
MDA21
P
226 G5M97080,G5M96980 MDA GBM
0 Mes female 68 131 D
r.,
MDA21
vi
,
537 G5M97067,G5M96967 MDA GBM
0 Mes male 59 32 D
r.,
MDA23
,
,
057 G5M97010,G5M97110 MDA GBM
0 Prolif male 57 70 D .
,
MDA23
,
445 G5M97064,G5M96964 MDA GBM
0 Mes male 49 59 D
MDA23
978 G5M97086,G5M96986 MDA GBM
1 Prolif female 32
MDA24
488 G5M97123,G5M97023 MDA GBM
0 Mes male 43 47 D
MDA24
Iv
710 G5M97093,G5M96993 MDA GBM
0 Mes male 54 125 D n
MDA24
1-3
843 S MDA GBM
0 Prolif male 17 120 D cp
n.)
MDA24
o
1-,
.6.
873 G5M96969,G5M97069 MDA GBM
0 Prolif male 82 55 D -,-:--,
c,
MDA25
--4
1-,
c:
266 G5M96985,G5M97085 MDA GBM
0 Prolif male 48 111 D oe
GEO_Accessions
Phillips Survival Censoring
id (U133A/U133B) Institution Histology
Anat. Site Recurrence Subclass Gender Age Weeks
Status
MDA25
0
n.)
450 GSM97008,GSM97108 MDA GBM
0 Mes male 39 53 D
1-,
vi
MDA26
-,-:--,
-4
18 GSM96950,GSM97050 MDA GBM
0 Mes male 60 131 D --4
--4
MDA28
n.)
vi
435 S MDA GBM
2 Unk male 12
MDA28
504 GSM97059,GSM96959 MDA GBM
0 Prolif male 55 238 D
MDA29
621 GSM96978,GSM97078 MDA GBM
0 Prolif male 57 242 A
MDA30
446 GSM97101,GSM97001 MDA GBM
1 Mes male 57
MDA30
P
617 G5M96976,G5M97076 MDA GBM
0 Prolif male 54 97 D
r.,
MDA31
vi
,
.6. 041 G5M97140,G5M97040 MDA GBM
0 Mes male 54 53 D
r.,
MDA31
,
,
220 G5M97128,G5M97028 MDA GBM
1 Mes male 54 .
,
MDA31
,
237 G5M96951,G5M97051 MDA GBM
0 Mes female 48 236 D
MDA31
472 G5M96998,G5M97098 MDA GBM
1 Mes female 32
MDA32
393 G5M97011,G5M97111 MDA GBM
0 Mes male 50 3 D
MDA33
Iv
044 G5M97091,G5M96991 MDA GBM
0 PN female 36 150 D n
MDA33
1-3
054 G5M96996,G5M97096 MDA GBM
0 Prolif female 43 12 D cp
n.)
MDA33
o
1-,
.6.
688 G5M97070,G5M96970 MDA GBM
0 Prolif male 41 59 D -,-:--,
c,
MDA33
--4
1-,
c:
825 G5M97141,G5M97041 MDA GBM
0 Mes male 54.1 53.1 D oe
GEO_Accessions
Phillips Survival Censoring
id (U133A/U133B) Institution Histology
Anat. Site Recurrence Subclass Gender Age Weeks
Status
MDA33
0
n.)
859 GSM96977,GSM97077 MDA GBM
0 Prolif male 40 95 D
1-,
vi
MDA34
-,-:--,
-4
061 GSM96988,GSM97088 MDA GBM
0 Mes male 55 57 D --4
--4
MDA34
n.)
vi
826 S MDA GBM
1 Mes male 14
MDA35
143 GSM96958,GSM97058 MDA GBM
0 Mes male 57 181 D
MDA35
312 GSM96981,GSM97081 MDA GBM
0 Mes male 47 77 D
MDA36
675 GSM96971,GSM97071 MDA GBM
1 Prolif male 45
MDA36
P
764 G5M96961,G5M97061 MDA GBM
0 Mes male 50 311 D
r.,
MDA37
vi
,
vi 775 G5M96965,G5M97065 MDA GBM
0 Mes male 48 97 D
r.,
MDA38
,
,
276 G5M96990,G5M97090 MDA GBM
0 PN female 53 62 D .
,
MDA38
,
490 G5M96992,G5M97092 MDA GBM
0 Mes male 48 154 A
MDA38
805 G5M96984,G5M97084 MDA GBM
0 Prolif female 34 16 D
MDA38
992 G5M97018,G5M97118 MDA GBM
0 PN male 24 145 A
MDA42
Iv
116 G5M96966,G5M97066 MDA GBM
0 Prolif male 44 33 D n
MDA42
1-3
411 G5M97009,G5M97109 MDA GBM
0 Prolif male 72 57 D cp
n.)
MDA42
o
1-,
.6.
6 G5M97126,G5M97026 MDA GBM
0 PN male 44 174 D -,-:--,
c,
MDA43
--4
1-,
c:
291 5 MDA GBM
2 Mes male 14 oe
GEO_Accessions
Phillips Survival Censoring
id (U133A/U133B) Institution Histology
Anat. Site Recurrence Subclass Gender Age Weeks
Status
MDA43
0
n.)
849 GSM97094,GSM96994 MDA GBM
0 Prolif female 32 39 D
1-,
vi
MDA44
-,-:--,
-4
33 GSM97019,GSM97119 MDA GBM
0 PN male 55 234 A --4
--4
MDA44
n.)
vi
442 GSM97062,GSM96962 MDA GBM
0 Prolif male 54 62 D
MDA47
399 GSM97006,GSM97106 MDA GBM
1 Mes female 72
MDA47
813 GSM97100,GSM97000 MDA GBM
0 Mes male 57 62 D
MDA48
078 GSM97104,GSM97004 MDA GBM
0 Mes female 72 65 D
MDA50
P
100 GSM96972,GSM97072 MDA GBM
0 Prolif female 43 210 A
r.,
MDA50
vi
,
c: 593 GSM97037,GSM97137 MDA GBM
0 PN female 49 73 D
r.,
MDA50
,
,
60 GSM97057,GSM96957 MDA GBM
1 Mes male 48 .
,
MDA53
,
520 GSM96968,GSM97068 MDA GBM
1 Prolif male 60
MDA54
336 GSM97083,GSM96983 MDA GBM
0 Prolif male 54 32 D
MDA56
075 GSM96974,GSM97074 MDA GBM
0 Prolif male 29 123 D
MDA56
Iv
270 GSM96982,GSM97082 MDA GBM
0 Mes female 48 56 D n
MDA57
1-3
49 GSM97054,GSM96954 MDA GBM
0 Prolif male 45 70 D cp
n.)
MDA63
o
1-,
.6.
26 GSM96995,GSM97095 MDA GBM
0 Prolif female 58 79 D -,-:--,
c,
MDA70
--4
1-,
c:
74 GSM97114,GSM97014 MDA GBM
0 PN female 22.1 353.6 A oe
GEO_Accessions
Phillips Survival Censoring
id (U133A/U133B) Institution Histology
Anat. Site Recurrence Subclass Gender Age Weeks
Status
MDA73
0
n.)
79 GSM97144,GSM97044 MDA
GBM 1 PN female 49
1¨,
vi
MDA82
- 4
77 GSM97063,GSM96963 MDA
GBM 0 PN male 34 203 D --4
--4
MDA83
n.)
vi
4 GSM96956,GSM97056 MDA
GBM 1 PN male 34
MDA86
62 S MDA GBM
0 Mes male 14 42 D
MDA93
92 GSM97132,GSM97032 MDA
GBM 1 PN male 23
MDA96
42 GSM97042,GSM97142 MDA
GBM 0 PN male 45 322 D
MDAN1
P
.
248 S MDA Normal
norm "
IV
MDAN1
vi
,
N,
--4 486 S MDA Normal
norm N,
MDAN1
,
,
818 S MDA Normal
norm .
,
MDAN2
,
512 S MDA Normal
norm
MDAN3
114 S MDA Normal
norm
MDAN3
116 S MDA Normal
norm
MDAN3
Iv
121 S MDA Normal
norm n
MDAN3
122 S MDA Normal
norm cp
n.)
o
non-neoplastic
.6.
N21A48 S UCSF Normal epileptic plug
norm
c:
non-neoplastic
--4
1¨,
c:
N3886 S UCSF Normal epileptic plug
norm oe
GEO_Accessions
Phillips Survival Censoring
id (U133A/U133B) Institution Histology
Anat. Site Recurrence Subclass Gender Age Weeks
Status
non-neoplastic
0
n.)
N7A41 S UCSF Normal epileptic plug
norm
1-,
vi
N88A_3 non-neoplastic
-a 5
- 4
4 S UCSF Normal epileptic plug
norm --4
--4
N99A_3 non-neoplastic
n.)
vi
6 S UCSF Normal epileptic plug
norm
Nichip1 Normal tissue from
6 S UCSF Normal GBM case
norm
SF0918 S UCSF GBM
PN male 42.4 54.9 D
SF0921 S UCSF GBM
Mes female 54.5 80.3 D
Cerebrum: Frontal
SF1166 S UCSF GBM lobe
PN female 42.6 28.9 D
P
Cerebrum: Parietal
.
r.,
SF1167 S UCSF GBM lobe
PN female 46.5 692.3 D ,
r.,
vi SF1198 S UCSF GBM
Unk male 54.9 18.3 D ,
r.,
oe
r.,
Cerebrum: Parietal
.
,
,
SF1368 S UCSF GBM lobe
Unk male 61.6 364.9 A .
'
Cerebrum: Frontal
.
,
SF1388 S UCSF GBM lobe
1 PN female 29 24.7 D
Cerebrum: Frontal
SF1461 S UCSF GBM lobe
Unk male 54.6 33.1 D
SF1475 S UCSF GBM
Unk female 42 22.3 D
Cerebrum: Parietal
SF1481 S UCSF GBM lobe
PN female 44.2 49 D
Cerebrum: Frontal
Iv
n
SF1547 S UCSF GBM lobe
Prolif female 35 33.6 D 1-3
Cerebrum: Frontal
cp
n.)
SF1605 S UCSF GBM Temporal lobe
Unk female 41 232 D o
1-,
.6.
Cerebrum: Parietal
-a 5
SF1653 S UCSF GBM lobe
Unk male 51.3 58.3 D c:
--4
1-,
Cerebrum: Frontal
c:
oe
SF1701 S UCSF GBM lobe
PN male 66.4 503.4 D
GEO_Accessions
Phillips Survival Censoring
id (U133A/U133B) Institution Histology
Anat. Site Recurrence Subclass Gender Age Weeks
Status
Cerebrum: Temporal
0
n.)
SF1750 S UCSF GBM lobe
Prolif female 45.1 67.7 D
1¨,
vi
Cerebrum: Frontal
-a 5
- 4
SF1751 S UCSF GBM lobe
PN female 38.3 70.4 D --4
--4
Cerebrum: Frontal
n.)
vi
SF1881 S UCSF GBM lobe
Mes male 54 5.3 D
Cerebrum: Temporal
SF1913 S UCSF GBM lobe
Mes male 47.6 82 D
Cerebrum: Frontal
SF2077 S UCSF GBM lobe
Unk male 66.3 141.1 D
Cerebrum: Frontal
SF2159 S UCSF GBM lobe
Unk male 43.2 47 D
Cerebrum: Temporal
P
SF2167 S UCSF GBM lobe
PN male 25.5 145.7 D
r.,
Cerebrum: Parietal
vi
,
SF2208 S UCSF GBM lobe
Unk female 50 9.1 D
r.,
Cerebrum: Frontal
,
,
SF2315 S UCSF GBM lobe
PN male 32.6 193 D .
,
Cerebrum: Frontal
,
SF2399 S UCSF GBM lobe
Unk male 38.9 50.4 D
Cerebrum: Frontal
SF2413 S UCSF GBM lobe
PN female 50.1 226.6 D
Cerebrum: Temporal
SF2434 S UCSF GBM lobe
Mes female 53.4 60.9 D
Cerebrum: Frontal
Iv
SF2560 S UCSF GBM lobe
Unk male 51.7 40.3 D n
Cerebrum: Temporal
SF2670 S UCSF GBM lobe
Mes male 51.1 31.3 D cp
n.)
o
Cerebrum: Temporal
SF2703 S UCSF GBM lobe
1 PN male 27.6 37.7 D -a 5
c:
Cerebrum: Frontal
--4
1¨,
c:
SF2704 S UCSF GBM lobe
Mes male 54.2 103.6 D oe
GEO_Accessions
Phillips Survival Censoring
id (U133A/U133B) Institution Histology
Anat. Site Recurrence Subclass Gender Age Weeks
Status
Cerebrum: Temporal
0
w
SF2737 S UCSF GBM lobe Mes
male 50 38.7 D
1¨,
cA
Cerebrum: Frontal
'a
--1
SF2760 S UCSF GBM Temporal lobe 0 Mes
male 47.5 97.1 D --1
--1
Cerebrum: Temporal
w
cA
SF2774 S UCSF GBM lobe Mes
male 37.6 83 D
Cerebrum: Temporal
SF2777 S UCSF GBM lobe PN
female 29.3 97.9 D
SF2894 S UCSF GBM Multifocal 0 Mes
male 44.6 14 D
Cerebrum: Frontal
SF2919 S UCSF GBM lobe Unk
male 44.7 46.1 D
Cerebrum: Parietal
SF2935 S UCSF GBM lobe 1 Unk
female 44.9 148 D P
2
Cerebrum: Frontal
c, SF2969 S UCSF GBM lobe
Unk female 34.9 24.9 D
Cerebrum: Temporal
..:SF3076 S UCSF GBM lobe Unk
male 237
,
. gs
:::::::::::::::::::::it$:u:b:rtilttettoi:0E0:::::::,,,,,,,,,,,,,,,,,,,,,,,:::::
::::::::,,,,,,,,,,,,,,,,,:::::::::::::::::::::::::::::::::::::,,,,,,,,,,,,,,,,,
,,,,,,,,,,:::::::::::::::::::::::::::::::::::::,,,,,,,,,,,,,,,,,,,,,,,:::::::::
::::::::::::::::::::::,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,::
:::,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,:::::,,,,,,,,,,,,,,,,,,,,,,,,,:
::::::::,,,,,,,:::::::::::::::::::::::::::::::::,,,,,,,,,,,,,,,::::::::::::::::
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::,,,,,,,,,,,,,,,,
,,,,,,,,,,,,,:::::::::::::::::::::::::::::::,,,,,,,,,,,,,,,,,,,,,::::::::::::::
::::::::::::::::
,
,
The following publications have additional clinical or molecular information
for some of these tumors: Phillips HS. et al. (2006) Molecular subclasses of
high-grade glioma predict prognosis, delineate a pattern of disease
progression, and resemble stages in neurogenesis. Cancer cell 9: 157-173. AND
Freij
'iWA. et al. (2004) Gene expression profiling of gliomas strongly predicts
survival. Cancer research 64: 6503-6510.
,-o
n
,-i
cp
w
=
4,.
'a
c,
--1
1-,
C'
00
CA 02923672 2016-03-07
WO 2015/077725
PCT/US2014/067168
Processing and analysis of microarray data
The PI3K/AKT pathway integrates information on cellular environment, energy
status,
stress and developmental stage to regulate apoptosis, autophagy, translation,
metabolism, stem
cell function and cell cycle [20], [22]. This involves multiple sites of
crosstalk with other
pathways. To capture the full function the inventors generated a gene list
that includes upstream
and downstream gene products that directly or indirectly regulate or are
regulated by AKT. This
includes: (1) proteins or members of protein complexes that bind to, modify or
regulate activity
or subcellular localization of AKT (2) proteins or members of protein
complexes phosphorylated
or regulated by AKT, (3) proteins known to regulate or be regulated directly
or indirectly by
AKT (e.g. AKT through MDM2 regulates levels of TP53 protein). These genes were
taken from:
(1) a database of AKT interacting proteins (BOND [23]), (2) a database of AKT
substrates
(http ://kinas puree .co .uk/Database/substrateList.php) (3) evidence
from Pubmed of
phosphorylation by AKT (search term AKT, January 2008), (4) evidence from
Pubmed that a
gene regulates or is regulated by AKT either directly or indirectly (search
term AKT, January
2008). Eliminating the genes with low variability across tumors within the
discovery dataset left
the 69 most variable genes used to classify AKT subgroups in the discovery
dataset (Table 2).
Five probes were not present in the validation dataset resulting in 64 of 69
AKT pathway genes
applied during validation (Table 2). In accordance with the present invention,
Table 2 lists non-
limiting examples of the various genes that may be used to cluster AKT
subgroups to diagnose
and define GBM.
Table 2: AKT pathway gene classifiers used for the discovery and validation
datasets
discovery validation
Akt Akt
pathway pathway
gene list gene list
ACLY ACLY ATP citrate lyase
AKT1 AKT1 V-akt nnurine thynnonna viral oncogene honnolog 1
ATXN1 ATXN1 Ataxin 1
BCL10 BCL10 B-cell CLL/Iynnphonna 10
CCND1 CCND1 Cyclin D1
CDC37 CDC37 Cell division cycle 37
CDKN1A CDKN1A Cyclin-dependent kinase inhibitor 1A (p21, Cip1)
CDKN1B CDKN1B Cyclin-dependent kinase inhibitor 1B (p27, Kip1)
61
CA 02923672 2016-03-07
WO 2015/077725
PCT/US2014/067168
CFD CFD Complement factor D (adipsin)
CHEK1 CHEK1 Checkpoint kinase 1
EGFR EGFR Epidermal growth factor receptor
ElF3B ElF3B Eukaryotic translation initiation factor 3, subunit B
ElF3E ElF3E Eukaryotic translation initiation factor 3, subunit E
ElF3G ElF3G Eukaryotic translation initiation factor 3, subunit G
ElF3H ElF3H Eukaryotic translation initiation factor 3, subunit H
ElF4EBP1 ElF4EBP1 Eukaryotic translation initiation factor 4E binding
protein 1
EPAS1 EPAS1 Endothelial PAS domain protein 1
EZH2 EZH2 Enhancer of zeste honnolog 2 (Drosophila)
FGFR2 FGFR2 Fibroblast growth factor receptor 2
FGFR3 FGFR3 Fibroblast growth factor receptor 3
FOX03 FOX03 Forkhead box 03
FYN FYN FYN oncogene related to SRC, FGR, YES
GAB1 GAB1 GRB2-associated binding protein 1
GAB2 GAB2 GRB2-associated binding protein 2
GRB10 GRB10 Growth factor receptor-bound protein 10
GSK3B GSK3B Glycogen synthase kinase 3 beta
HIF1A HIF1A Hypoxia inducible factor 1, alpha subunit
HSP90AB1 HSP90AB1 Heat shock protein 90 alpha (cytosolic), class B member 1
HSP90B1 HSP90B1 Heat shock protein 90kDa beta (Grp94), member 1
INPP5D INPP5D Inositol polyphosphate-5-phosphatase, 145kDa
IRS1 IRS1 Insulin receptor substrate 1
IR52 IR52 Insulin receptor substrate 2
KDR KDR Kinase insert domain receptor (a type III receptor tyrosine
kinase)
KRAS KRAS V-Ki-ras2 Kirsten rat sarcoma viral oncogene honnolog
MAP3K5 MAP3K5 Mitogen-activated protein kinase kinase kinase 5
MAPK8IP1 MAPK8IP1 Mitogen-activated protein kinase 8 interacting protein 1
NRAS NRAS Neuroblastonna RAS viral (v-ras) oncogene honnolog
PALLD PALLD Palladin, cytoskeletal associated protein
PDGFA PDGFA Platelet-derived growth factor alpha polypeptide
PDGFC PDGFC Platelet derived growth factor C
PDGFD PDGFD Platelet derived growth factor D
PDGFRB PDGFRB Platelet-derived growth factor receptor, beta polypeptide
PDK1 PDK1 3-phosphoinositide dependent protein kinase-1
PHLPP PHLPP1 PH domain and leucine rich repeat protein phosphatase 1
PIK3C2B PIK3C2B Phosphatidylinosito1-4-phosphate 3-kinase, catalytic
subunit type 2 beta
PIK3CA PIK3CA Phosphatidylinosito1-4,5-bisphosphate 3-kinase, catalytic
subunit alpha
PIK3R1 PIK3R1 Phosphoinositide-3-kinase, regulatory subunit 1 (alpha)
PKD2 PKD2 Polycystic kidney disease 2 (autosonnal dominant)
PKN2 PKN2 Protein kinase N2
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PPARGC1A PPARGC1A Peroxisonne proliferator-activated receptor gamma,
coactivator 1 alpha
PPP2R1A PPP2R1A Protein phosphatase 2, regulatory subunit A, alpha
PPP2R2B PPP2R2B Protein phosphatase 2, regulatory subunit B, beta
RAF1 RAF1 V-raf-1 nnurine leukemia viral oncogene honnolog 1
SFRS1 SRSF1 Serine/arginine-rich splicing factor 1
SORBS2 SORBS2 Sorbin and SH3 domain containing 2
SSB SSB Sjogren syndrome antigen B (autoantigen La)
SYK SYK Spleen tyrosine kinase
TP53 TP53 Tumor protein p53
TRIB3 TRIB3 Tribbles honnolog 3 (Drosophila)
TSC1 TSC1 Tuberous sclerosis 1
TSC2 TSC2 Tuberous sclerosis 2
TWIST1 TWIST1 Twist basic helix-loop-helix transcription factor 1
VIM VIM Vinnentin
WNK1 WNK1 WNK lysine deficient protein kinase 1
AKT1S1 AKT1 substrate 1 (proline-rich)
IGF2 Insulin-like growth factor 2 (sonnatonnedin A)
PPP2R2C Protein phosphatase 2, regulatory subunit B, gamma
RICTOR RPTOR independent companion of MTOR, complex 2
YBX1 Y box binding protein 1
The inventors isolated patient subgroups in the discovery dataset using RMA
normalized
and median centered data [24]. The inventors applied consensus k-means
clustering with the
Pearson's correlation coefficient as the similarity (1-distance) and complete
linkage with 10,000
iterations using a sub-sampling ratio of 0.8. The inventors then plotted the
consensus distribution
function (CDF) to find the optimal number of AKT subgroups [25]. Silhouette
width values were
computed for each sample [26] and only samples with a positive silhouette
width were used in
further analyses.
The inventors isolated AKT subgroups in the TCGA validation dataset using raw
data
preprocessed as described for the discovery dataset. TCGA samples were mapped
onto AKT
subgroups in the discovery dataset by adapting the k means clustering
algorithm. First, the
inventors found boundaries for each AKT subgroup in the discovery set by
calculating the
pairwise correlation coefficients between all samples within a subgroup. The
minimum pairwise
correlation coefficient was used as the lower boundary for each subgroup. TCGA
samples were
classified by computing the correlation coefficient between each TCGA and
GBM195 sample.
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TCGA samples were assigned to an AKT subgroup if the average pairwise
correlation
coefficient with members of the group was greater than the lower boundary of
that group. Ties
were resolved by selecting the closest cluster.
Analysis of GO terms
Conventional Gene Ontology (GO) enrichment analysis was dominated by generic
GBM
biological processes; therefore the inventors used a single-sample approach
analogous to the
method used by Verhaak and Barbie [10]. To identify GO biological processes
enriched within
each individual sample the inventors applied the hypergeometric test with
Benjamini and
Hochberg's correction on all expressed genes (using a two-fold change
threshold from the
median to determine up- and down-regulated genes). Neurodevelopmental terms
enriched in >
20% of tumors were considered for analysis.
Analysis of aCGH data
The GISTIC algorithm [27] was applied to the 456 TCGA samples with copy number
information and results visualized using the Integrated Genomic Viewer (IGV)
[28] to find copy
number alterations (CNA) in the validation set. Broad copy number alterations
in the discovery
dataset were found as described previously [29] using a customized version of
the Sanger CNV
database [http://www.sanger.ac.uk/research/areas/humangenetics/cnvi. For
experiments that
compare broad CNA in the discovery and validation dataset the inventors
identified broad copy
number alterations in the validation dataset as follows. Briefly, the
inventors found the average q
value (generated from the GISTIC algorithm) for 15 genes spaced evenly across
the region of
interest. If > 50% of genes had a q value less than expected by chance after
correcting for
multiple testing (q < 0.25), that region was called as a copy number
alteration.
Reverse Phase Protein Arrays
Level 3 (median centered, normalized, Z transformed) reverse phase protein
array
(RPPA) data was downloaded from the cBio Cancer Genomics Portal
(http://www.cbioportal.org/public-portal/). One hundred and eighty six of the
215 tumors with
RPPA data could be assigned to an AKT class and were used for analysis.
Correlation
coefficients between two antibodies against the same protein were high
indicating adequate
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antibody specificity and pre-processing of data (Pearson correlation
coefficient = 0.83-0.98 for
antibody pairs (GSK3A/B pS9/21, MAPK1, FOX03, GATA3, S338 p-RAF1).
Statistics
Differences between one subgroup and the rest were assessed using the F test
for clinical
variables and the likelihood ratio test for categorical variables. The
Bonferroni method [30] was
applied to correct for multiple hypotheses. The inventors applied the Tukey
HSD test to find
pairwise differences between groups and correct for multiple comparisons [31].
Survival
differences between subgroups were assessed using the Chi-squared test. Age
was added to build
a multivariate Cox model. For survival comparisons of BCNU/CCNU treatment
between
to
subgroups there were not enough observations to correct for age. After
deleting all observations
younger than 45, survival was no longer related to age. Significance was then
determined using
log rank. The Pearson goodness-of-fit test was used to assess the null
hypothesis that proportions
of G-CIMP tumors by subgroup and recurrent tumors by subgroup are equal to the
proportions
for all tumors by subgroup. P-values for these tests were calculated by Monte
Carlo simulation
since the counts of tumors by subgroup were too small to apply the large
sample chi-square
approximation. If the null hypothesis was rejected, then standardized
residuals were used to
determine which subgroups showed significant differences.
Example 2: AKT Pathway Genes Define 5 Prognostic Subgroups in Glioblastoma
AKT pathway gene expression divides GBM into at least six subgroups
The inventors investigated AKT pathway variations in GBM by developing a list
of AKT
pathway genes (Table 2) then applying consensus clustering for the number of
clusters k = 2 to
10 (Figure 9; Figure lA shows results for k = 5 to 8). The inventors evaluated
cluster stability
using the consensus cumulative distribution function (CDF) plot of the
consensus index (Figure
1C) [25]. Cluster stability increased for k = 2 to 6 but not appreciably for
k> 6 (Figure 1C);
suggesting six is the optimum number of GBM AKT subgroups. Silhouette width
values were
computed for each sample [26] (Figure 1B) and samples with a positive
silhouette width were
selected for further analyses.
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The inventors aim to have a classification system where clinical differences
are
maximized. Here, the inventors investigated how survival of patient subgroups
varies with k.
Figure 1D plots the corrected p value between the longest and shortest
surviving subgroups for
each k. p values were low for k = 3 and 6; k = 6 was the lowest (Figure 1D).
This supports the
CDF results selecting 6 clusters. The 6 consensus k-means subgroups were named
AKT cluster 1
(AKT Cl; AKT subgroup 1), AKT proneural (AKT PN; AKT subgroup 2), AKT
mesenchymal
(AKT MES; AKT subgroup 3), AKT classical (AKT CLAS; AKT subgroup 4), AKT
secondary-
like (AKT SL; AKT subgroup 5) and AKT proliferative (AKT PROLIF; AKT subgroup
6) based
on their molecular and clinical features and prior naming [4], [32].
Validation of AKT subgroups in an independent dataset
The inventors next validated AKT subgroups in an independent dataset of non-
overlapping samples. TCGA samples were mapped onto discovery AKT subgroups by
assigning
a sample to the closest Akt subtype, as described in the methods section. Only
two samples were
assigned to AKT subgroup Cl, therefore this subgroup was dropped from all
further analysis.
Figure 2 compares AKT pathway gene expression in the discovery (Figure 2A) and
validation
(Figure 2B) sets. It shows the pattern of expression of AKT pathway genes
within subgroups is
similar in both datasets. Interestingly, the PN subgroup in both datasets
contained all non-
neoplastic samples (not shown). The inventors examined expression of AKT
pathway genes in
subgroups (Figure 10). These data show AKT classes arise from complex patterns
of gene
expression in subgroups. It did not point to a role for a specific part of the
AKT pathway within
any subgroup.
The inventors next investigated correspondence between copy number alterations
(CNA)
in AKT subgroups from discovery (Figure 2C) and validation (Figure 2D)
datasets. The PN
subgroup was omitted since it had no CNA information in the discovery dataset.
CNA within
subgroups were similar in the discovery and validation datasets: a high
percentage of tumors
with 7gain/10 loss occurred in every subgroup except SL, the SL subgroup had
greater frequency
of 19q loss and the CLAS subgroup had increased gain of chrl9q relative to the
rest. Therefore
all subgroup-associated trends in CNA within the discovery dataset were
recapitulated in the
validation dataset.
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TCGA, Phillips and G-CIMP subgroups distribute non-randomly in AKT subgroups
Phillips, TCGA and G-CIMP subgroups distributed non-randomly in AKT subgroups
(Figure 3A, B and C; Figures 12 and 13). There was a tendency for AKT
subtyping to split each
Phillips subgroup in two. The AKT PN and SL subtypes were significantly
enriched in the
Phillips PN subtype (Figure 3A, Figure 12; p < 0.5 Bonferroni corrected). The
AKT MES and
CLAS subtypes were significantly enriched in Phillips MES subtype (Figure 3A,
Figure 12, p <
0.5; Bonferroni corrected). The AKT PROLIF subtype was significantly enriched
in the Phillips
PROLIF subtype (Figure 3A, Figure 12; p < 0.5; Bonferroni corrected). The
enrichment of
Phillips PROLIF tumors in AKT Cl subtype did not reach significance. AKT
subgroups had less
concordance with TCGA subgroups [10]. AKT SL and PROLIF subtypes were
significantly
enriched in TCGA PN subtype; while AKT MES and CL subgroups were enriched in
the TCGA
MES and CL subtype, respectively (Figure 3B, Figure 13; p < 0.5; Bonferroni
corrected). The
AKT PN subtype was a mixture of all the TCGA subgroups. The AKT SL and PROLIF
subgroups contained the majority of G-CIMP tumors (Figure 3C). Taken together
these data
show AKT classification divides existing subgroups further.
Patients in the SL subgroup are younger and have longer survival
AKT subgroups have different clinical characteristics (Figure 4B and D;
Figures 12 and
13). SL patients in the discovery dataset had longer median survival (3.9 vs.
1.05 yrs.; p =
0.0005; Figure 4b; SL vs. the rest) and were younger (median age = 38 vs. 49;
SL vs. total; p =
0.05 using Tukey HSD test to correct for multiple comparisons; Figure 12).
After adjusting for
age in Cox multivariate analysis, SL status remained a significant predictor
of survival (p =
0.027; SL vs. the rest). The PROLIF subgroup had statistically significant
shorter survival than
the rest (0.75 vs. 1.25 yrs.; p = 0.0029; Figure 4B) although age of these
patients was not
different than all patients (median age = 49 vs. 49 years; PROLIF vs. total;
Figure 12). Although
the magnitude was diminished, a similar trend was observed for SL patients in
the validation
dataset for survival (1.67 vs. 1.1 yrs.; p = .003 SL vs. rest; Figure 4D) and
age (median age = 49
vs. 59 yrs.; p = .07; SL vs. total, Figure 13) although the age difference was
not statistically
significant. In comparison, patient subgroups defined using Phillips (Figure
4A) and TCGA
(Figure 4C) methods using the same database have no statistically significant
differences in
survival.
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Consistent with the less aggressive character of SL tumors, there was a trend
toward
decreased endothelial proliferation (46% vs. 66%; p = 0.017 vs. rest;
uncorrected), and
palisading necrosis (10% vs. 51%; p = 0.07 vs. rest; uncorrected) in the
validation dataset (Figure
13). There were similar trends in the discovery set although they also did not
reach significance
(Figure 12). Taken together these data show subgroups in the discovery and
validation datasets
have similar clinical features. It also shows AKT subtypes have distinct
clinical characteristics.
Evidence AKT subtyping is a predictive marker for sensitivity to BCNU/CCNU
Survival differences between subgroups suggest AKT subtypes are either
prognostic or
predictive (forecasts tumor aggressiveness or response to therapy,
respectively). Since AKT
to influences response to chemotherapy [33], while not wishing to be bound
by any theory, the
inventors believe AKT subgroups are predictive markers. Indeed, TCGA SL
patients treated with
BCNU or CCNU had longer median survival than those receiving other treatments
(Figure 5;
median survival = 5.8 vs. 1.05 years; p = 0.03 after correcting for age; log
rank). Those receiving
BCNU or CCNU were older and had less IDH1 mutations than those that didn't
(median age =
54 vs. 49 years; % with IDH1 mutations = 17% vs. 32%; with vs. without
BCNU/CCNU
respectively); indicating age and IDH1 mutation status do not account their
increased survival.
This finding indicates patients in the SL subgroup are sensitive to BCNU and
CCNU.
Subgroups have distinct genomic alterations
The inventors used TCGA data to investigate how molecular alterations
partition in
subgroups. All subgroups had unique broad (Figure 6A; Figure 11) and/or focal
(Figures 14 and
15) DNA CNA. The CLAS subtype was enriched in broad CNA previously associated
with more
aggressive tumors such as loss of chromosome regions 6q and gain of 19q and
20q [34] (Figure
6A). The SL subtype was enriched in broad CNA associated with better prognosis
(loss of 19q;
Figure 6A) [34]. Each subgroup had unique focal CNA (Figures 14 and 15). This
data shows
AKT subtyping groups tumors with similar molecular characteristics.
An integrated analysis of mutations, CNA and mRNA expression in glioma-
associated
genes shows some AKT subgroups had similar features as TCGA subgroups (Figure
6B). The
AKT CLAS subgroup was significantly enriched in alterations in EGFR and CDKN2A
similar to
TCGA CLAS subgroup [10]. The AKT MES subtype was characterized by mutations in
NF1
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and RB1 and increased mRNA for the mesenchymal marker, MET, similar to the
TCGA MES
subgroup [10], although these did not reach statistical significance. The SL
subtype was enriched
in IDH1 mutations (42% vs 3% SL vs. rest) and GCIMP (47% vs. 4%; SL vs. rest)
although only
the enrichment in IDH1 mutant tumors was significant. The PROLIF subtype was
also slightly
enriched in IDH1 mutations (11%) in this dataset containing 218 validated
samples. However
that dropped to 7% when considering all TCGA tumors with IDH1 mutation
information (not
shown). Both the SL and PROLIF subgroups were also enriched in alterations
found more
frequently in secondary tumors including TP53 mutations and increased mRNA and
CN gains
for PDGFRA. The PROLIF was distinguished from SL subtype by an increase in
mutations and
copy number alterations in EGFR and CDKN2A (Figure 6B) and enrichment in
recurrent tumors
(18% vs 8%; PROLIF vs rest; Figure 13). Genomic alterations in other
RTK/RAS/PI3K/AKT
pathway members were either not significantly enriched in any subgroup (PTEN,
PIK3R1, MET,
SPRY2; Figure 6B) or the frequency was too low to evaluate (ERBB2, KRAS, NRAS,
HRAS,
PIK3CA, FOX01, FOX03, AKT1, AKT2, AKT3; not shown); although MET mRNA was
enriched and SPRY2 mRNA was low in the MES and CLAS subtypes, respectively
(Figure 6B).
Taken together these data suggest involvement of oncogenic and tumor
suppressor pathways can
differ between subgroups.
Subgroups have distinct patterns of expression for PI3K/AKT/mTOR components
The inventors find subgroups have distinct patterns of expression of mRNA
(Figure 7A),
protein and phospho-proteins (Figure 7B) for PI3K/AKT/mTOR pathway components.
The most
notable patterns were in the MES and SL subgroups. The MES subtype had
decreased expression
for inhibitors of mTOR, AKT and PI3K (TSC2 and p-AMPK protein; TSC1, TSC2,
PHLPP1,
PHLPP2 and PI3KR1 message). Consistent with increased activity of the
AKT/mTOR/S6 axis,
this subgroup also had elevated p-S6 (Figure 7B) and a high positive
correlation between p-AKT
and p-S6 (Figure 7C). The long surviving SL subgroup had the opposite pattern
of expression;
high expression of AKT and mTOR inhibitors (Figure 7A and B), decreased
expression of pS6
(Figure 7B) and lower correlation between pAKT and pS6 (Figure 7C). The
inventors' proposed
pathway map for the MES and SL subgroups (7D) based on this data posits how
expression of
pathway inhibitors affects output of the AKT/mTOR/S6 axis. This data indicates
subgroups will
have different sensitivities to pathway inhibitors.
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GO terms suggest subgroups have a different dominant biological process and
cell of origin
The inventors used Gene Ontology (GO) to investigate the biological role of
genes
expressed in tumors and how terms partition in subgroups. Each subgroup,
except CLAS, had a
high percentage of tumors with functionally related terms that suggested a
different dominate
biological process (Table 3). The CLAS subgroup had a mixture of terms. Each
subgroup also
had GO terms associated with neurodevelopment (Table 3; highlighted with
bolded text;
summarized in Figure 8B). The PN and CLAS subgroups had only terms associated
with
neurogenesis suggesting a committed neural precursor cell of origin. The MES,
SL and PROLIF
subgroups had terms associated with both neuro- and glio-genesis suggesting a
stem cell or early
uncommitted progenitor cell of origin. These data suggest the cell of origin
and dominant
biological process can differ in subgroups.
Table 3: GO term analysis of genes differentially expressed in subgroups
Cl (2 Samples)
Proportion Biological
Biological Process Name
of Samples Process
100% GO:0000087 M phase of mitotic cell cycle
100% GO:0000236 mitotic pronnetaphase
100% GO:0000278 mitotic cell cycle
100% GO:0000279 M phase
100% GO:0000280 nuclear division
100% GO:0007067 mitosis
100% GO:0022402 cell cycle process
100% GO:0022403 cell cycle phase
100% GO:0048285 organelle fission
50% GO:0006336 DNA replication-independent nucleosonne assembly
50% GO:0007051 spindle organization
50% GO:0007059 chromosome segregation
50% GO:0007091 mitotic metaphase/anaphase transition
50% GO:0007094 mitotic cell cycle spindle assembly checkpoint
50% GO:0030071 regulation of mitotic metaphase/anaphase
transition
50% GO:0031055 chromatin remodeling at centronnere
50% GO:0031577 spindle checkpoint
50% GO:0034080 CenH3-containing nucleosonne assembly at
centronnere
50% GO:0034724 DNA replication-independent nucleosonne
organization
50% GO:0043486 histone exchange
50% GO:0045841 negative regulation of mitotic metaphase/anaphase
transition
50% GO:0046826 negative regulation of protein export from nucleus
50% GO:0051301 cell division
50% GO:0051983 regulation of chromosome segregation
50% GO:0071173 spindle assembly checkpoint
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50% GO:0071174 mitotic cell cycle spindle checkpoint
PN (30 Samples)
Proportion Biological
Biological Process Name
of Samples Process
100% GO:0001505 regulation of neurotransmitter levels
100% GO:0003001 generation of a signal involved in cell-cell
signaling
100% GO:0006836 neurotransmitter transport
100% GO:0007268 synaptic transmission
100% GO:0007269 neurotransmitter secretion
100% GO:0014047 glutamate secretion
100% GO:0019226 transmission of nerve impulse
100% GO:0023061 signal release
100% GO:0035637 nnulticellular organisnnal signaling
100% GO:0048489 synaptic vesicle transport
97% GO:0007267 cell-cell signaling
97% GO:0031644 regulation of neurological system process
97% GO:0050877 neurological system process
97% GO:0051969 regulation of transmission of nerve impulse
93% GO:0050804 regulation of synaptic transmission
90% GO:0007399 nervous system development
90% GO:0016079 synaptic vesicle exocytosis
87% GO:0032940 secretion by cell
83% GO:0048167 regulation of synaptic plasticity
80% GO:0022008 neurogenesis
80% GO:0030182 neuron differentiation
77% GO:0048667 cell morphogenesis involved in neuron differentiation
77% GO:0048699 generation of neurons
77% GO:0048812 neuron projection nnorphogenesis
73% GO:0007409 axonogenesis
73% GO:0031175 neuron projection development
73% GO:0048666 neuron development
67% GO:0000904 cell nnorphogenesis involved in differentiation
63% GO:0007611 learning or memory
63% GO:0030030 cell projection organization
63% GO:0048858 cell projection nnorphogenesis
60% GO:0003008 system process
60% GO:0032990 cell part nnorphogenesis
60% GO:0048488 synaptic vesicle endocytosis
57% GO:0042391 regulation of membrane potential
57% GO:0046903 secretion
57% GO:0050890 cognition
53% GO:0007612 learning
50% GO:0006887 exocytosis
50% GO:0007214 gamma-anninobutyric acid signaling pathway
47% GO:0044057 regulation of system process
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47% GO:0048168 regulation of neuronal synaptic plasticity
47% GO:0050773 regulation of dendrite development
43% GO:0002504 antigen processing and presentation of peptide or
polysaccharide antigen
................... via MHC class ll
43% GO:0007610 behavior
40% GO:0000902 cell nnorphogenesis
40% GO:0051899 membrane depolarization
40% GO:0060333 interferon-gamma-mediated signaling pathway
37% GO:0090072 positive regulation of sodium ion transport via
voltage-gated sodium
channel activity
33% GO:0010243 response to organic nitrogen
33% GO:0060627 regulation of vesicle-mediated transport
30% GO:0007272 ensheathnnent of neurons
30% GO:0008366 axon ensheathnnent
30% GO:0071346 cellular response to interferon-gamma
27% GO:0017157 regulation of exocytosis
27% GO:0032989 cellular component nnorphogenesis
27% GO:0034341 response to interferon-gamma
27% GO:0042552 nnyelination
23% GO:0001508 regulation of action potential
23% GO:0019228 regulation of action potential in neuron
23% GO:0051592 response to calcium ion
23% GO:0055082 cellular chemical homeostasis
20% GO:0006873 cellular ion homeostasis
20% GO:0010975 regulation of neuron projection development
17% GO:0006821 chloride transport
17% GO:0010970 nnicrotubule-based transport
17% GO:0048468 cell development
13% GO:0006413 translational initiation
13% GO:0006415 translational termination
13% GO:0006614 SRP-dependent cotranslational protein targeting to
membrane
13% GO:0008088 axon cargo transport
13% GO:0015698 inorganic anion transport
13% GO:0019080 viral genonne expression
13% GO:0019083 viral transcription
13% GO:0019725 cellular homeostasis
13% GO:0043241 protein complex disassembly
13% GO:0043624 cellular protein complex disassembly
13% GO:0045047 protein targeting to ER
13% GO:0060079 regulation of excitatory postsynaptic membrane
potential
13% GO:0060314 regulation of ryanodine-sensitive calcium-release
channel activity
13% GO:0070972 protein localization in endoplasnnic reticulunn
13% GO:0072599 establishment of protein localization in endoplasnnic
reticulunn
10% GO:0002480 antigen processing and presentation of exogenous
peptide antigen via
MHC class I, TAP-independent
10% GO:0006414 translational elongation
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10% GO:0006612 protein targeting to membrane
10% GO:0006613 cotranslational protein targeting to membrane
10% GO:0009263 deoxyribonucleotide biosynthetic process
10% GO:0010001 glial cell differentiation
10% GO:0014075 response to amine stimulus
10% GO:0019058 viral infectious cycle
10% GO:0022411 cellular component disassembly
10% GO:0023052 signaling
10% GO:0030001 metal ion transport
10% GO:0030168 platelet activation
10% GO:0030705 cytoskeleton-dependent intracellular transport
10% GO:0031344 regulation of cell projection organization
10% GO:0031646 positive regulation of neurological system process
10% GO:0032984 nnacronnolecular complex disassembly
10% GO:0034623 cellular nnacronnolecular complex disassembly
10% GO:0042063 gliogenesis
10% GO:0048709 oligodendrocyte differentiation
10% GO:0050805 negative regulation of synaptic transmission
10% GO:0050806 positive regulation of synaptic transmission
10% GO:0051049 regulation of transport
10% GO:0051823 regulation of synapse structural plasticity
10% GO:0051971 positive regulation of transmission of nerve impulse
10% GO:0071417 cellular response to organic nitrogen
10% GO:0071418 cellular response to amine stimulus
10% GO:0071845 cellular component disassembly at cellular level
10% GO:0072594 establishment of protein localization to organelle
7% GO:0000184 nuclear-transcribed nnRNA catabolic process, nonsense-
mediated decay
7% GO:0002495 antigen processing and presentation of peptide
antigen via MHC class ll
7% GO:0006820 anion transport
7% GO:0007154 cell communication
7% GO:0014003 oligodendrocyte development
7% GO:0015800 acidic amino acid transport
7% GO:0016081 synaptic vesicle docking involved in exocytosis
7% GO:0017156 calcium ion-dependent exocytosis
7% GO:0019886 antigen processing and presentation of exogenous
peptide antigen via
MHC class ll
7% GO:0022010 central nervous system nnyelination
7% GO:0022415 viral reproductive process
7% GO:0030224 nnonocyte differentiation
7% GO:0031111 negative regulation of nnicrotubule polymerization or
depolynnerization
7% GO:0032291 axon ensheathnnent in central nervous system
7% GO:0034340 response to type I interferon
7% GO:0042274 ribosomal small subunit biogenesis
7% GO:0043090 amino acid import
7% GO:0043092 L-amino acid import
7% GO:0048169 regulation of long-term neuronal synaptic plasticity
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7% GO:0060337 type I interferon-mediated signaling pathway
7% GO:0065008 regulation of biological quality
7% GO:0071229 cellular response to acid
7% GO:0071357 cellular response to type I interferon
3% GO:0000956 nuclear-transcribed nnRNA catabolic process
3% GO:0001101 response to acid
3% GO:0001504 neurotransmitter uptake
3% GO:0001766 membrane raft polarization
3% GO:0001915 negative regulation of T cell mediated cytotoxicity
3% GO:0002237 response to molecule of bacterial origin
3% GO:0002246 wound healing involved in inflammatory response
3% GO:0002250 adaptive immune response
3% GO:0002252 immune effector process
3% GO:0002253 activation of immune response
3% GO:0002376 immune system process
3% GO:0002429 immune response-activating cell surface receptor
signaling pathway
3% GO:0002443 leukocyte mediated immunity
3% GO:0002449 lymphocyte mediated immunity
3% GO:0002455 hunnoral immune response mediated by circulating
innnnunoglobulin
3% GO:0002460 adaptive immune response based on somatic recombination
of immune
receptors built from innnnunoglobulin superfannily domains
3% GO:0002474 antigen processing and presentation of peptide
antigen via MHC class I
3% GO:0002478 antigen processing and presentation of exogenous
peptide antigen
3% GO:0002479 antigen processing and presentation of exogenous
peptide antigen via
MHC class I, TAP-dependent
3% GO:0002682 regulation of immune system process
3% GO:0002683 negative regulation of immune system process
3% GO:0002684 positive regulation of immune system process
3% GO:0002685 regulation of leukocyte migration
3% GO:0002686 negative regulation of leukocyte migration
3% GO:0002688 regulation of leukocyte chennotaxis
3% GO:0002689 negative regulation of leukocyte chennotaxis
3% GO:0002694 regulation of leukocyte activation
3% GO:0002696 positive regulation of leukocyte activation
3% GO:0002757 immune response-activating signal transduction
3% GO:0002764 immune response-regulating signaling pathway
3% GO:0002768 immune response-regulating cell surface receptor
signaling pathway
3% GO:0006401 RNA catabolic process
3% GO:0006402 nnRNA catabolic process
3% GO:0006412 translation
3% GO:0006605 protein targeting
3% GO:0006826 iron ion transport
3% GO:0006886 intracellular protein transport
3% GO:0006935 chennotaxis
3% GO:0006952 defense response
3% GO:0006954 inflammatory response
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3% GO:0006955 immune response
3% GO:0006956 complement activation
3% GO:0006958 complement activation, classical pathway
3% GO:0006959 hunnoral immune response
3% GO:0007026 negative regulation of nnicrotubule depolynnerization
3% GO:0007417 central nervous system development
3% GO:0009265 2'-deoxyribonucleotide biosynthetic process
3% GO:0009607 response to biotic stimulus
3% GO:0009611 response to wounding
3% GO:0009615 response to virus
3% GO:0009617 response to bacterium
3% GO:0009914 hormone transport
3% GO:0015682 ferric iron transport
3% GO:0015813 L-glutamate transport
3% GO:0015988 energy coupled proton transport, against
electrochemical gradient
3% GO:0015991 ATP hydrolysis coupled proton transport
3% GO:0016064 innnnunoglobulin mediated immune response
3% GO:0016188 synaptic vesicle maturation
3% GO:0019724 B cell mediated immunity
3% GO:0019882 antigen processing and presentation
3% GO:0019884 antigen processing and presentation of exogenous
antigen
3% GO:0021675 nerve development
3% GO:0021782 glial cell development
3% GO:0030198 extracellular matrix organization
3% GO:0030199 collagen fibril organization
3% GO:0030334 regulation of cell migration
3% GO:0030534 adult behavior
3% GO:0030595 leukocyte chennotaxis
3% GO:0031102 neuron projection regeneration
3% GO:0031114 regulation of nnicrotubule depolynnerization
3% GO:0031294 lymphocyte costinnulation
3% GO:0031295 T cell costinnulation
3% GO:0031345 negative regulation of cell projection organization
3% GO:0031580 membrane raft distribution
3% GO:0031645 negative regulation of neurological system process
3% GO:0032101 regulation of response to external stimulus
3% GO:0032103 positive regulation of response to external stimulus
3% GO:0032496 response to lipopolysaccharide
3% GO:0033124 regulation of GTP catabolic process
3% GO:0033365 protein localization to organelle
3% GO:0033572 transferrin transport
3% GO:0034097 response to cytokine stimulus
3% GO:0040012 regulation of locomotion
3% GO:0042330 taxis
3% GO:0042493 response to drug
3% GO:0042590 antigen processing and presentation of exogenous
peptide antigen via
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................... MHC class I
3% GO:0042592 homeostatic process
3% GO:0043062 extracellular structure organization
3% GO:0043087 regulation of GTPase activity
3% GO:0043200 response to amino acid stimulus
3% GO:0043242 negative regulation of protein complex disassembly
3% GO:0043368 positive T cell selection
3% GO:0045059 positive thymic T cell selection
3% GO:0045061 thymic T cell selection
3% GO:0045087 innate immune response
3% GO:0045163 clustering of voltage-gated potassium channels
3% GO:0045663 positive regulation of nnyoblast differentiation
3% GO:0045730 respiratory burst
3% GO:0045766 positive regulation of angiogenesis
3% GO:0046928 regulation of neurotransmitter secretion
3% GO:0048002 antigen processing and presentation of peptide
antigen
3% GO:0048015 phosphatidylinositol-mediated signaling
3% GO:0048017 inositol lipid-mediated signaling
3% GO:0048583 regulation of response to stimulus
3% GO:0048584 positive regulation of response to stimulus
3% GO:0048678 response to axon injury
3% GO:0048731 system development
3% GO:0048878 chemical homeostasis
3% GO:0050776 regulation of immune response
3% GO:0050778 positive regulation of immune response
3% GO:0050795 regulation of behavior
3% GO:0050801 ion homeostasis
3% GO:0050851 antigen receptor-mediated signaling pathway
3% GO:0050863 regulation of T cell activation
3% GO:0050865 regulation of cell activation
3% GO:0050867 positive regulation of cell activation
3% GO:0050870 positive regulation of T cell activation
3% GO:0050920 regulation of chennotaxis
3% GO:0050921 positive regulation of chennotaxis
3% GO:0051050 positive regulation of transport
3% GO:0051056 regulation of small GTPase mediated signal
transduction
3% GO:0051129 negative regulation of cellular component
organization
3% GO:0051239 regulation of nnulticellular organisnnal process
3% GO:0051249 regulation of lymphocyte activation
3% GO:0051665 membrane raft localization
3% GO:0051707 response to other organism
3% GO:0051938 L-glutamate import
3% GO:0051970 negative regulation of transmission of nerve impulse
3% GO:0060078 regulation of postsynaptic membrane potential
3% GO:0060326 cell chennotaxis
3% GO:0060384 innervation
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3% GO:0070098 chennokine-mediated signaling pathway
3% GO:0071205 protein localization to juxtaparanode region of axon
3% GO:0071219 cellular response to molecule of bacterial origin
3% GO:0071222 cellular response to lipopolysaccharide
3% GO:0071230 cellular response to amino acid stimulus
3% GO:0071402 cellular response to lipoprotein particle stimulus
3% GO:0072012 glonnerulus vasculature development
3% GO:0072239 nnetanephric glonnerulus vasculature development
3% GO:0090025 regulation of nnonocyte chennotaxis
3% GO:2000145 regulation of cell motility
3% GO:2000300 regulation of synaptic vesicle exocytosis
MES (34 Samples)
Proportion Biological
Biological Process Name
of Samples Process
68% GO:0006952 defense response
68% GO:0009611 response to wounding
65% GO:0006955 immune response
65% GO:0045087 innate immune response
62% GO:0002376 immune system process
62% GO:0051707 response to other organism
59% GO:0006954 inflammatory response
59% GO:0007155 cell adhesion
59% GO:0009607 response to biotic stimulus
59% GO:0022610 biological adhesion
56% GO:0002504 antigen processing and presentation of peptide or
polysaccharide antigen
................... via MHC class ll
56% GO:0009617 response to bacterium
56% GO:0034341 response to interferon-gamma
53% GO:0002250 adaptive immune response
53% GO:0002460 adaptive immune response based on somatic recombination
of immune
receptors built from innnnunoglobulin superfannily domains
53% GO:0006956 complement activation
53% GO:0006959 hunnoral immune response
53% GO:0016064 innnnunoglobulin mediated immune response
53% GO:0019724 B cell mediated immunity
53% GO:0030198 extracellular matrix organization
53% GO:0043062 extracellular structure organization
53% GO:0045765 regulation of angiogenesis
53% GO:0050900 leukocyte migration
50% GO:0002237 response to molecule of bacterial origin
50% GO:0002252 immune effector process
50% GO:0002253 activation of immune response
50% GO:0006950 response to stress
50% GO:0032496 response to lipopolysaccharide
50% GO:0034097 response to cytokine stimulus
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50% GO:0040011 locomotion
50% GO:0071346 cellular response to interferon-gamma
47% GO:0001568 blood vessel development
47% GO:0001944 vasculature development
47% GO:0002443 leukocyte mediated immunity
47% GO:0016477 cell migration
47% GO:0030199 collagen fibril organization
47% GO:0032101 regulation of response to external stimulus
47% GO:0043200 response to amino acid stimulus
47% GO:0050776 regulation of immune response
44% GO:0001101 response to acid
44% GO:0002449 lymphocyte mediated immunity
44% GO:0002684 positive regulation of immune system process
44% GO:0006928 cellular component movement
44% GO:0006935 chennotaxis
44% GO:0009605 response to external stimulus
44% GO:0010033 response to organic substance
44% GO:0030334 regulation of cell migration
44% GO:0042060 wound healing
44% GO:0042330 taxis
44% GO:0050778 positive regulation of immune response
41% GO:0002576 platelet degranulation
41% GO:0002682 regulation of immune system process
41% GO:0006958 complement activation, classical pathway
41% GO:0010243 response to organic nitrogen
41% GO:0022603 regulation of anatomical structure nnorphogenesis
41% GO:0040017 positive regulation of locomotion
41% GO:0042221 response to chemical stimulus
41% GO:0048731 system development
41% GO:0048870 cell motility
41% GO:0051674 localization of cell
41% GO:0060326 cell chennotaxis
41% GO:0060333 interferon-gamma-mediated signaling pathway
38% GO:0002455 hunnoral immune response mediated by circulating
innnnunoglobulin
38% GO:0002495 antigen processing and presentation of peptide
antigen via MHC class ll
38% GO:0002685 regulation of leukocyte migration
38% GO:0009612 response to mechanical stimulus
38% GO:0019886 antigen processing and presentation of exogenous
peptide antigen via
MHC class ll
38% GO:0030595 leukocyte chennotaxis
38% GO:0040012 regulation of locomotion
38% GO:0050920 regulation of chennotaxis
38% GO:0051272 positive regulation of cellular component movement
38% GO:0072358 cardiovascular system development
38% GO:0072359 circulatory system development
38% GO:0072376 protein activation cascade
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38% GO:2000145 regulation of cell motility
35% GO:0001775 cell activation
35% GO:0007399 nervous system development
35% GO:0030155 regulation of cell adhesion
35% GO:0030335 positive regulation of cell migration
35% GO:0031960 response to corticosteroid stimulus
35% GO:0048468 cell development
35% GO:0048583 regulation of response to stimulus
35% GO:0051239 regulation of nnulticellular organisnnal process
35% GO:0051270 regulation of cellular component movement
35% GO:2000147 positive regulation of cell motility
32% GO:0001525 angiogenesis
32% GO:0002764 immune response-regulating signaling pathway
32% GO:0007275 nnulticellular organisnnal development
32% GO:0009653 anatomical structure nnorphogenesis
32% GO:0014075 response to amine stimulus
32% GO:0042742 defense response to bacterium
32% GO:0048514 blood vessel nnorphogenesis
32% GO:0048584 positive regulation of response to stimulus
32% GO:0048856 anatomical structure development
32% GO:0050793 regulation of developmental process
32% GO:0050921 positive regulation of chennotaxis
32% GO:0051384 response to glucocorticoid stimulus
32% GO:0055093 response to hyperoxia
32% GO:0070482 response to oxygen levels
29% GO:0000904 cell nnorphogenesis involved in differentiation
29% GO:0002544 chronic inflammatory response
29% GO:0002688 regulation of leukocyte chennotaxis
29% GO:0002757 immune response-activating signal transduction
29% GO:0007162 negative regulation of cell adhesion
29% GO:0019221 cytokine-mediated signaling pathway
29% GO:0031099 regeneration
29% GO:0031294 lymphocyte costinnulation
29% GO:0031295 T cell costinnulation
29% GO:0042063 gliogenesis
29% GO:0050870 positive regulation of T cell activation
29% GO:0071222 cellular response to lipopolysaccharide
29% GO:0071229 cellular response to acid
29% GO:2000026 regulation of nnulticellular organisnnal development
26% GO:0002768 immune response-regulating cell surface receptor
signaling pathway
26% GO:0006909 phagocytosis
26% GO:0010035 response to inorganic substance
26% GO:0016525 negative regulation of angiogenesis
26% GO:0022008 neurogenesis
26% GO:0030168 platelet activation
26% GO:0030182 neuron differentiation
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26% GO:0031175 neuron projection development
26% GO:0032103 positive regulation of response to external stimulus
26% GO:0032940 secretion by cell
26% GO:0032964 collagen biosynthetic process
26% GO:0042127 regulation of cell proliferation
26% GO:0048812 neuron projection nnorphogenesis
26% GO:0051704 multi-organism process
26% GO:0065008 regulation of biological quality
26% GO:0070887 cellular response to chemical stimulus
26% GO:0071216 cellular response to biotic stimulus
26% GO:0071219 cellular response to molecule of bacterial origin
26% GO:0071345 cellular response to cytokine stimulus
24% GO:0002429 immune response-activating cell surface receptor
signaling pathway
24% GO:0002687 positive regulation of leukocyte migration
24% GO:0007568 aging
24% GO:0007596 blood coagulation
24% GO:0007599 hennostasis
24% GO:0008360 regulation of cell shape
24% GO:0014070 response to organic cyclic compound
24% GO:0030593 neutrophil chennotaxis
24% GO:0032502 developmental process
24% GO:0033628 regulation of cell adhesion mediated by integrin
24% GO:0045766 positive regulation of angiogenesis
24% GO:0048545 response to steroid hormone stimulus
24% GO:0048585 negative regulation of response to stimulus
24% GO:0048666 neuron development
24% GO:0048667 cell morphogenesis involved in neuron differentiation
24% GO:0050730 regulation of peptidyl-tyrosine phosphorylation
24% GO:0050817 coagulation
24% GO:0050865 regulation of cell activation
24% GO:0050867 positive regulation of cell activation
24% GO:0071230 cellular response to amino acid stimulus
21% GO:0000302 response to reactive oxygen species
21% GO:0001666 response to hypoxia
21% GO:0001817 regulation of cytokine production
21% GO:0002274 myeloid leukocyte activation
21% GO:0002690 positive regulation of leukocyte chennotaxis
21% GO:0002694 regulation of leukocyte activation
21% GO:0007409 axonogenesis
21% GO:0009719 response to endogenous stimulus
21% GO:0009888 tissue development
21% GO:0018149 peptide cross-linking
21% GO:0030030 cell projection organization
21% GO:0032570 response to progesterone stimulus
21% GO:0032989 cellular component nnorphogenesis
21% GO:0048660 regulation of smooth muscle cell proliferation
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21% GO:0048699 generation of neurons
21% GO:0048771 tissue remodeling
21% GO:0048858 cell projection nnorphogenesis
21% GO:0050727 regulation of inflammatory response
21% GO:0050732 negative regulation of peptidyl-tyrosine
phosphorylation
21% GO:0050795 regulation of behavior
21% GO:0050851 antigen receptor-mediated signaling pathway
21% GO:0050863 regulation of T cell activation
21% GO:0051094 positive regulation of developmental process
21% GO:0051249 regulation of lymphocyte activation
21% GO:0051251 positive regulation of lymphocyte activation
21% GO:0060337 type I interferon-mediated signaling pathway
21% GO:0071357 cellular response to type I interferon
18% GO:0000902 cell nnorphogenesis
18% GO:0001501 skeletal system development
18% GO:0002696 positive regulation of leukocyte activation
18% GO:0006887 exocytosis
18% GO:0010038 response to metal ion
18% GO:0010574 regulation of vascular endothelial growth factor
production
18% GO:0019228 regulation of action potential in neuron
18% GO:0030154 cell differentiation
18% GO:0032501 nnulticellular organisnnal process
18% GO:0032963 collagen metabolic process
18% GO:0032990 cell part nnorphogenesis
18% GO:0034340 response to type I interferon
18% GO:0045059 positive thymic T cell selection
18% GO:0045730 respiratory burst
18% GO:0048513 organ development
18% GO:0048520 positive regulation of behavior
18% GO:0050878 regulation of body fluid levels
18% GO:0051128 regulation of cellular component organization
18% GO:0061041 regulation of wound healing
18% GO:0070372 regulation of ERK1 and ERK2 cascade
18% GO:0071418 cellular response to amine stimulus
15% GO:0001503 ossification
15% GO:0002683 negative regulation of immune system process
15% GO:0006879 cellular iron ion homeostasis
15% GO:0006957 complement activation, alternative pathway
15% GO:0008284 positive regulation of cell proliferation
15% GO:0010466 negative regulation of peptidase activity
15% GO:0016337 cell-cell adhesion
15% GO:0042493 response to drug
15% GO:0045321 leukocyte activation
15% GO:0046903 secretion
15% GO:0048646 anatomical structure formation involved in
nnorphogenesis
15% GO:0048869 cellular developmental process
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15% GO:0050852 T cell receptor signaling pathway
15% GO:0050896 response to stimulus
15% GO:0055072 iron ion homeostasis
15% GO:0060548 negative regulation of cell death
15% GO:0071310 cellular response to organic substance
15% GO:0071675 regulation of mononuclear cell migration
15% GO:2000097 regulation of smooth muscle cell-matrix adhesion
12% GO:0001819 positive regulation of cytokine production
12% GO:0001936 regulation of endothelial cell proliferation
12% GO:0002697 regulation of immune effector process
12% GO:0007159 leukocyte cell-cell adhesion
12% GO:0007229 integrin-mediated signaling pathway
12% GO:0007417 central nervous system development
12% GO:0008285 negative regulation of cell proliferation
12% GO:0009628 response to abiotic stimulus
12% GO:0010951 negative regulation of endopeptidase activity
12% GO:0019882 antigen processing and presentation
12% GO:0030097 hennopoiesis
12% GO:0030193 regulation of blood coagulation
12% GO:0031100 organ regeneration
12% GO:0031102 neuron projection regeneration
12% GO:0035767 endothelial cell chennotaxis
12% GO:0042542 response to hydrogen peroxide
12% GO:0043542 endothelial cell migration
12% GO:0044259 nnulticellular organisnnal macromolecule metabolic
process
12% GO:0045582 positive regulation of T cell differentiation
12% GO:0050678 regulation of epithelial cell proliferation
12% GO:0050764 regulation of phagocytosis
12% GO:0050804 regulation of synaptic transmission
12% GO:0050853 B cell receptor signaling pathway
12% GO:0051093 negative regulation of developmental process
12% GO:0052547 regulation of peptidase activity
12% GO:0055082 cellular chemical homeostasis
12% GO:0071417 cellular response to organic nitrogen
12% GO:0090022 regulation of neutrophil chennotaxis
12% GO:1900046 regulation of hennostasis
9% GO:0001505 regulation of neurotransmitter levels
9% GO:0001933 negative regulation of protein phosphorylation
9% GO:0002275 myeloid cell activation involved in immune response
9% GO:0002520 immune system development
9% GO:0002699 positive regulation of immune effector process
9% GO:0002886 regulation of myeloid leukocyte mediated immunity
9% GO:0002920 regulation of hunnoral immune response
9% GO:0003013 circulatory system process
9% GO:0006836 neurotransmitter transport
9% GO:0006873 cellular ion homeostasis
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9% GO:0006875 cellular metal ion homeostasis
9% GO:0006897 endocytosis
9% GO:0007267 cell-cell signaling
9% GO:0007268 synaptic transmission
9% GO:0007272 ensheathnnent of neurons
9% GO:0008015 blood circulation
9% GO:0008366 axon ensheathnnent
9% GO:0009887 organ nnorphogenesis
9% GO:0009968 negative regulation of signal transduction
9% GO:0009991 response to extracellular stimulus
9% GO:0010001 glial cell differentiation
9% GO:0010324 membrane invagination
9% GO:0010332 response to gamma radiation
9% GO:0010543 regulation of platelet activation
9% GO:0010646 regulation of cell communication
9% GO:0010648 negative regulation of cell communication
9% GO:0010758 regulation of macrophage chennotaxis
9% GO:0010759 positive regulation of macrophage chennotaxis
9% GO:0010810 regulation of cell-substrate adhesion
9% GO:0010812 negative regulation of cell-substrate adhesion
9% GO:0014910 regulation of smooth muscle cell migration
9% GO:0019226 transmission of nerve impulse
9% GO:0019800 peptide cross-linking via chondroitin 4-sulfate
glycosanninoglycan
9% GO:0021529 spinal cord oligodendrocyte cell differentiation
9% GO:0021530 spinal cord oligodendrocyte cell fate specification
9% GO:0023051 regulation of signaling
9% GO:0023057 negative regulation of signaling
9% GO:0030003 cellular cation homeostasis
9% GO:0030098 lymphocyte differentiation
9% GO:0030323 respiratory tube development
9% GO:0030324 lung development
9% GO:0031644 regulation of neurological system process
9% GO:0031663 lipopolysaccharide-mediated signaling pathway
9% GO:0032835 glonnerulus development
9% GO:0032944 regulation of mononuclear cell proliferation
9% GO:0035637 nnulticellular organisnnal signaling
9% GO:0042102 positive regulation of T cell proliferation
9% GO:0043066 negative regulation of apoptotic process
9% GO:0043069 negative regulation of programmed cell death
9% GO:0043368 positive T cell selection
9% GO:0044057 regulation of system process
9% GO:0044087 regulation of cellular component biogenesis
9% GO:0044236 nnulticellular organisnnal metabolic process
9% GO:0045058 T cell selection
9% GO:0045597 positive regulation of cell differentiation
9% GO:0045621 positive regulation of lymphocyte differentiation
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9% GO:0046635 positive regulation of alpha-beta T cell activation
9% GO:0048534 hennopoietic or lymphoid organ development
9% GO:0050670 regulation of lymphocyte proliferation
9% GO:0050729 positive regulation of inflammatory response
9% GO:0051240 positive regulation of nnulticellular organisnnal
process
9% GO:0051969 regulation of transmission of nerve impulse
9% GO:0055001 muscle cell development
9% GO:0055002 striated muscle cell development
9% GO:0055065 metal ion homeostasis
9% GO:0070098 chennokine-mediated signaling pathway
9% GO:0070208 protein heterotrinnerization
9% GO:0070663 regulation of leukocyte proliferation
9% GO:0071622 regulation of granulocyte chennotaxis
9% GO:0071901 negative regulation of protein serine/threonine
kinase activity
9% GO:0090090 negative regulation of canonical Wnt receptor
signaling pathway
6% GO:0000041 transition metal ion transport
6% GO:0000188 inactivation of MAPK activity
6% GO:0001504 neurotransmitter uptake
6% GO:0001508 regulation of action potential
6% GO:0001763 nnorphogenesis of a branching structure
6% GO:0001776 leukocyte homeostasis
6% GO:0001782 B cell homeostasis
6% GO:0001953 negative regulation of cell-matrix adhesion
6% GO:0002260 lymphocyte homeostasis
6% GO:0002521 leukocyte differentiation
6% GO:0002686 negative regulation of leukocyte migration
6% GO:0002698 negative regulation of immune effector process
6% GO:0002819 regulation of adaptive immune response
6% GO:0002821 positive regulation of adaptive immune response
6% GO:0002822 regulation of adaptive immune response based on
somatic recombination
................... of immune receptors built from innnnunoglobulin
superfannily domains
6% GO:0002824 positive regulation of adaptive immune response based
on somatic
recombination of immune receptors built from innnnunoglobulin
................... superfannily domains
6% GO:0003008 system process
6% GO:0003094 glonnerular filtration
6% GO:0006469 negative regulation of protein kinase activity
6% GO:0006911 phagocytosis, engulfment
6% GO:0006916 anti-apoptosis
6% GO:0007269 neurotransmitter secretion
6% GO:0007411 axon guidance
6% GO:0007566 embryo implantation
6% GO:0009266 response to temperature stimulus
6% GO:0009306 protein secretion
6% GO:0009615 response to virus
6% GO:0009725 response to hormone stimulus
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6% GO:0009743 response to carbohydrate stimulus
6% GO:0009966 regulation of signal transduction
6% GO:0010575 positive regulation vascular endothelial growth factor
production
6% GO:0010594 regulation of endothelial cell migration
6% GO:0010769 regulation of cell nnorphogenesis involved in
differentiation
6% GO:0010955 negative regulation of protein processing
6% GO:0014052 regulation of gamma-anninobutyric acid secretion
6% GO:0014706 striated muscle tissue development
6% GO:0014805 smooth muscle adaptation
6% GO:0014829 vascular smooth muscle contraction
6% GO:0019725 cellular homeostasis
6% GO:0021545 cranial nerve development
6% GO:0021781 glial cell fate commitment
6% GO:0022604 regulation of cell nnorphogenesis
6% GO:0022904 respiratory electron transport chain
6% GO:0030029 actin filament-based process
6% GO:0030111 regulation of Wnt receptor signaling pathway
6% GO:0030178 negative regulation of Wnt receptor signaling pathway
6% GO:0030217 T cell differentiation
6% GO:0030224 nnonocyte differentiation
6% GO:0031347 regulation of defense response
6% GO:0031348 negative regulation of defense response
6% GO:0031349 positive regulation of defense response
6% GO:0031579 membrane raft organization
6% GO:0031589 cell-substrate adhesion
6% GO:0031646 positive regulation of neurological system process
6% GO:0031915 positive regulation of synaptic plasticity
6% GO:0032102 negative regulation of response to external stimulus
6% GO:0032355 response to estradiol stimulus
6% GO:0032642 regulation of chennokine production
6% GO:0032760 positive regulation of tumor necrosis factor
production
6% GO:0033003 regulation of mast cell activation
6% GO:0033006 regulation of mast cell activation involved in immune
response
6% GO:0033673 negative regulation of kinase activity
6% GO:0034059 response to anoxia
6% GO:0034614 cellular response to reactive oxygen species
6% GO:0035457 cellular response to interferon-alpha
6% GO:0040007 growth
6% GO:0042129 regulation of T cell proliferation
6% GO:0042246 tissue regeneration
6% GO:0042326 negative regulation of phosphorylation
6% GO:0042327 positive regulation of phosphorylation
6% GO:0042552 nnyelination
6% GO:0042592 homeostatic process
6% GO:0042692 muscle cell differentiation
6% GO:0043304 regulation of mast cell degranulation
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6% GO:0043407 negative regulation of MAP kinase activity
6% GO:0043408 regulation of MAPK cascade
6% GO:0043409 negative regulation of MAPK cascade
6% GO:0043627 response to estrogen stimulus
6% GO:0045123 cellular extravasation
6% GO:0045333 cellular respiration
6% GO:0045576 mast cell activation
6% GO:0045586 regulation of gamma-delta T cell differentiation
6% GO:0045588 positive regulation of gamma-delta T cell
differentiation
6% GO:0045664 regulation of neuron differentiation
6% GO:0045906 negative regulation of vasoconstriction
6% GO:0046649 lymphocyte activation
6% GO:0048010 vascular endothelial growth factor receptor signaling
pathway
6% GO:0048167 regulation of synaptic plasticity
6% GO:0048247 lymphocyte chennotaxis
6% GO:0048286 lung alveolus development
6% GO:0048661 positive regulation of smooth muscle cell
proliferation
6% GO:0048709 oligodendrocyte differentiation
6% GO:0048747 muscle fiber development
6% GO:0048872 homeostasis of number of cells
6% GO:0048878 chemical homeostasis
6% GO:0050654 chondroitin sulfate proteoglycan metabolic process
6% GO:0050679 positive regulation of epithelial cell proliferation
6% GO:0050777 negative regulation of immune response
6% GO:0050801 ion homeostasis
6% GO:0050818 regulation of coagulation
6% GO:0050864 regulation of B cell activation
6% GO:0050877 neurological system process
6% GO:0051146 striated muscle cell differentiation
6% GO:0051216 cartilage development
6% GO:0051346 negative regulation of hydrolase activity
6% GO:0051348 negative regulation of transferase activity
6% GO:0051591 response to cAMP
6% GO:0051592 response to calcium ion
6% GO:0051971 positive regulation of transmission of nerve impulse
6% GO:0055006 cardiac cell development
6% GO:0055013 cardiac muscle cell development
6% GO:0055080 cation homeostasis
6% GO:0060056 mammary gland involution
6% GO:0060071 Wnt receptor signaling pathway, planar cell polarity
pathway
6% GO:0060284 regulation of cell development
6% GO:0060348 bone development
6% GO:0060537 muscle tissue development
6% GO:0060541 respiratory system development
6% GO:0070374 positive regulation of ERK1 and ERK2 cascade
6% GO:0070665 positive regulation of leukocyte proliferation
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6% GO:0072012 glonnerulus vasculature development
6% GO:0080134 regulation of response to stress
6% GO:0090175 regulation of establishment of planar polarity
6% GO:0097066 response to thyroid hormone stimulus
6% GO:0097067 cellular response to thyroid hormone stimulus
6% GO:0097205 renal filtration
6% GO:2000377 regulation of reactive oxygen species metabolic
process
3% GO:0000272 polysaccharide catabolic process
3% GO:0001300 chronological cell aging
3% GO:0001523 retinoid metabolic process
3% GO:0001562 response to protozoan
3% GO:0001569 patterning of blood vessels
3% GO:0001570 vasculogenesis
3% GO:0001649 osteoblast differentiation
3% GO:0001656 nnetanephros development
3% GO:0001706 endoderm formation
3% GO:0001754 eye photoreceptor cell differentiation
3% GO:0001766 membrane raft polarization
3% GO:0001774 nnicroglial cell activation
3% GO:0001816 cytokine production
3% GO:0001822 kidney development
3% GO:0001838 embryonic epithelial tube formation
3% GO:0001843 neural tube closure
3% GO:0001878 response to yeast
3% GO:0001894 tissue homeostasis
3% GO:0001938 positive regulation of endothelial cell proliferation
3% GO:0001957 intrannennbranous ossification
3% GO:0001974 blood vessel remodeling
3% GO:0002009 nnorphogenesis of an epithelium
3% GO:0002062 chondrocyte differentiation
3% GO:0002064 epithelial cell development
3% GO:0002138 retinoic acid biosynthetic process
3% GO:0002218 activation of innate immune response
3% GO:0002238 response to molecule of fungal origin
3% GO:0002263 cell activation involved in immune response
3% GO:0002279 mast cell activation involved in immune response
3% GO:0002281 macrophage activation involved in immune response
3% GO:0002282 nnicroglial cell activation involved in immune
response
3% GO:0002283 neutrophil activation involved in immune response
3% GO:0002366 leukocyte activation involved in immune response
3% GO:0002431 Fc receptor mediated stimulatory signaling pathway
3% GO:0002444 myeloid leukocyte mediated immunity
3% GO:0002448 mast cell mediated immunity
3% GO:0002478 antigen processing and presentation of exogenous
peptide antigen
3% GO:0002507 tolerance induction
3% GO:0002526 acute inflammatory response
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3% GO:0002532 production of molecular mediator involved in
inflammatory response
3% GO:0002543 activation of blood coagulation via clotting cascade
3% GO:0002577 regulation of antigen processing and presentation
3% GO:0002634 regulation of germinal center formation
3% GO:0002673 regulation of acute inflammatory response
3% GO:0002675 positive regulation of acute inflammatory response
3% GO:0002679 respiratory burst involved in defense response
3% GO:0002689 negative regulation of leukocyte chennotaxis
3% GO:0002700 regulation of production of molecular mediator of
immune response
3% GO:0002703 regulation of leukocyte mediated immunity
3% GO:0002705 positive regulation of leukocyte mediated immunity
3% GO:0002708 positive regulation of lymphocyte mediated immunity
3% GO:0002820 negative regulation of adaptive immune response
3% GO:0003007 heart nnorphogenesis
3% GO:0003009 skeletal muscle contraction
3% GO:0003012 muscle system process
3% GO:0003073 regulation of systemic arterial blood pressure
3% GO:0003081 regulation of systemic arterial blood pressure by
renin-angiotensin
3% GO:0003158 endothelium development
3% GO:0003205 cardiac chamber development
3% GO:0003206 cardiac chamber nnorphogenesis
3% GO:0003208 cardiac ventricle nnorphogenesis
3% GO:0003231 cardiac ventricle development
3% GO:0003382 epithelial cell nnorphogenesis
3% GO:0005976 polysaccharide metabolic process
3% GO:0006006 glucose metabolic process
3% GO:0006022 anninoglycan metabolic process
3% GO:0006029 proteoglycan metabolic process
3% GO:0006090 pyruvate metabolic process
3% GO:0006096 glycolysis
3% GO:0006120 nnitochondrial electron transport, NADH to ubiquinone
3% GO:0006599 phosphagen metabolic process
3% GO:0006600 creatine metabolic process
3% GO:0006633 fatty acid biosynthetic process
3% GO:0006690 icosanoid metabolic process
3% GO:0006720 isoprenoid metabolic process
3% GO:0006790 sulfur compound metabolic process
3% GO:0006826 iron ion transport
3% GO:0006910 phagocytosis, recognition
3% GO:0006929 substrate-dependent cell migration
3% GO:0006936 muscle contraction
3% GO:0006937 regulation of muscle contraction
3% GO:0006941 striated muscle contraction
3% GO:0006968 cellular defense response
3% GO:0006979 response to oxidative stress
3% GO:0007026 negative regulation of nnicrotubule depolynnerization
88
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3% GO:0007132 meiotic metaphase I
3% GO:0007154 cell communication
3% GO:0007157 heterophilic cell-cell adhesion
3% GO:0007160 cell-matrix adhesion
3% GO:0007165 signal transduction
3% GO:0007166 cell surface receptor signaling pathway
3% GO:0007199 G-protein signaling, coupled to cGMP nucleotide
second messenger
3% GO:0007263 nitric oxide mediated signal transduction
3% GO:0007422 peripheral nervous system development
3% GO:0007507 heart development
3% GO:0007517 muscle organ development
3% GO:0007519 skeletal muscle tissue development
3% GO:0007584 response to nutrient
3% GO:0007589 body fluid secretion
3% GO:0007610 behavior
3% GO:0007611 learning or memory
3% GO:0007612 learning
3% GO:0008217 regulation of blood pressure
3% GO:0008277 regulation of G-protein coupled receptor protein
signaling pathway
3% GO:0008283 cell proliferation
3% GO:0008347 glial cell migration
3% GO:0009620 response to fungus
3% GO:0009746 response to hexose stimulus
3% GO:0009756 carbohydrate mediated signaling
3% GO:0010172 embryonic body nnorphogenesis
3% GO:0010212 response to ionizing radiation
3% GO:0010447 response to acidity
3% GO:0010561 negative regulation of glycoprotein biosynthetic
process
3% GO:0010563 negative regulation of phosphorus metabolic process
3% GO:0010595 positive regulation of endothelial cell migration
3% GO:0010740 positive regulation of intracellular protein kinase
cascade
3% GO:0010811 positive regulation of cell-substrate adhesion
3% GO:0010927 cellular component assembly involved in
nnorphogenesis
3% GO:0010939 regulation of necrotic cell death
3% GO:0010975 regulation of neuron projection development
3% GO:0014003 oligodendrocyte development
3% GO:0014013 regulation of gliogenesis
3% GO:0014020 primary neural tube formation
3% GO:0014047 glutamate secretion
3% GO:0014068 positive regulation of phosphatidylinositol 3-kinase
cascade
3% GO:0014820 tonic smooth muscle contraction
3% GO:0015682 ferric iron transport
3% GO:0016049 cell growth
3% GO:0016101 diterpenoid metabolic process
3% GO:0016331 nnorphogenesis of embryonic epithelium
3% GO:0016339 calcium-dependent cell-cell adhesion
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3% GO:0018108 peptidyl-tyrosine phosphorylation
3% GO:0018212 peptidyl-tyrosine modification
3% GO:0019220 regulation of phosphate metabolic process
3% GO:0019229 regulation of vasoconstriction
3% GO:0019302 D-ribose biosynthetic process
3% GO:0019693 ribose phosphate metabolic process
3% GO:0019827 stem cell maintenance
3% GO:0019884 antigen processing and presentation of exogenous
antigen
3% GO:0021542 dentate gyrus development
3% GO:0021602 cranial nerve nnorphogenesis
3% GO:0021675 nerve development
3% GO:0021782 glial cell development
3% GO:0022614 membrane to membrane docking
3% GO:0022900 electron transport chain
3% GO:0023052 signaling
3% GO:0030036 actin cytoskeleton organization
3% GO:0030048 actin filament-based movement
3% GO:0030049 muscle filament sliding
3% GO:0030194 positive regulation of blood coagulation
3% GO:0030204 chondroitin sulfate metabolic process
3% GO:0030225 macrophage differentiation
3% GO:0030239 myofibril assembly
3% GO:0030240 skeletal muscle thin filament assembly
3% GO:0030278 regulation of ossification
3% GO:0030336 negative regulation of cell migration
3% GO:0030855 epithelial cell differentiation
3% GO:0031032 actonnyosin structure organization
3% GO:0031112 positive regulation of nnicrotubule polymerization or
depolynnerization
3% GO:0031113 regulation of nnicrotubule polymerization
3% GO:0031116 positive regulation of nnicrotubule polymerization
3% GO:0031344 regulation of cell projection organization
3% GO:0031345 negative regulation of cell projection organization
3% GO:0031394 positive regulation of prostaglandin biosynthetic
process
3% GO:0031580 membrane raft distribution
3% GO:0031664 regulation of lipopolysaccharide-mediated signaling
pathway
3% GO:0031667 response to nutrient levels
3% GO:0032649 regulation of interferon-gamma production
3% GO:0032675 regulation of interleukin-6 production
3% GO:0032677 regulation of interleukin-8 production
3% GO:0032879 regulation of localization
3% GO:0032928 regulation of superoxide anion generation
3% GO:0032930 positive regulation of superoxide anion generation
3% GO:0032946 positive regulation of mononuclear cell proliferation
3% GO:0032956 regulation of actin cytoskeleton organization
3% GO:0032970 regulation of actin filament-based process
3% GO:0033275 actin-myosin filament sliding
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3% GO:0033572 transferrin transport
3% GO:0033630 positive regulation of cell adhesion mediated by
integrin
3% GO:0033993 response to lipid
3% GO:0034121 regulation of toll-like receptor signaling pathway
3% GO:0034136 negative regulation of toll-like receptor 2 signaling
pathway
3% GO:0034284 response to nnonosaccharide stimulus
3% GO:0034329 cell junction assembly
3% GO:0034330 cell junction organization
3% GO:0034612 response to tumor necrosis factor
3% GO:0034637 cellular carbohydrate biosynthetic process
3% GO:0034755 iron ion transnnennbrane transport
3% GO:0035148 tube formation
3% GO:0035239 tube nnorphogenesis
3% GO:0035295 tube development
3% GO:0035385 Roundabout signaling pathway
3% GO:0035583 sequestering of TGFbeta in extracellular matrix
3% GO:0035860 glial cell-derived neurotrophic factor receptor
signaling pathway
3% GO:0035924 cellular response to vascular endothelial growth
factor stimulus
3% GO:0036072 direct ossification
3% GO:0040013 negative regulation of locomotion
3% GO:0042035 regulation of cytokine biosynthetic process
3% GO:0042108 positive regulation of cytokine biosynthetic process
3% GO:0042110 T cell activation
3% GO:0042116 macrophage activation
3% GO:0042384 cilium assembly
3% GO:0042391 regulation of membrane potential
3% GO:0042730 fibrinolysis
3% GO:0042743 hydrogen peroxide metabolic process
3% GO:0042832 defense response to protozoan
3% GO:0043092 L-amino acid import
3% GO:0043270 positive regulation of ion transport
3% GO:0043277 apoptotic cell clearance
3% GO:0043279 response to alkaloid
3% GO:0043299 leukocyte degranulation
3% GO:0043303 mast cell degranulation
3% GO:0043383 negative T cell selection
3% GO:0043405 regulation of MAP kinase activity
3% GO:0043410 positive regulation of MAPK cascade
3% GO:0043535 regulation of blood vessel endothelial cell migration
3% GO:0043536 positive regulation of blood vessel endothelial cell
migration
3% GO:0043549 regulation of kinase activity
3% GO:0044319 wound healing, spreading of cells
3% GO:0045055 regulated secretory pathway
3% GO:0045060 negative thymic T cell selection
3% GO:0045061 thymic T cell selection
3% GO:0045088 regulation of innate immune response
91
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3% GO:0045089 positive regulation of innate immune response
3% GO:0045446 endothelial cell differentiation
3% GO:0045595 regulation of cell differentiation
3% GO:0045596 negative regulation of cell differentiation
3% GO:0045619 regulation of lymphocyte differentiation
3% GO:0045638 negative regulation of myeloid cell differentiation
3% GO:0045667 regulation of osteoblast differentiation
3% GO:0045785 positive regulation of cell adhesion
3% GO:0045859 regulation of protein kinase activity
3% GO:0045923 positive regulation of fatty acid metabolic process
3% GO:0045936 negative regulation of phosphate metabolic process
3% GO:0046364 nnonosaccharide biosynthetic process
3% GO:0046390 ribose phosphate biosynthetic process
3% GO:0046456 icosanoid biosynthetic process
3% GO:0046530 photoreceptor cell differentiation
3% GO:0046634 regulation of alpha-beta T cell activation
3% GO:0046643 regulation of gamma-delta T cell activation
3% GO:0046645 positive regulation of gamma-delta T cell activation
3% GO:0048002 antigen processing and presentation of peptide
antigen
3% GO:0048168 regulation of neuronal synaptic plasticity
3% GO:0048488 synaptic vesicle endocytosis
3% GO:0048489 synaptic vesicle transport
3% GO:0048518 positive regulation of biological process
3% GO:0048519 negative regulation of biological process
3% GO:0048522 positive regulation of cellular process
3% GO:0048589 developmental growth
3% GO:0048638 regulation of developmental growth
3% GO:0048644 muscle organ nnorphogenesis
3% GO:0048662 negative regulation of smooth muscle cell
proliferation
3% GO:0048678 response to axon injury
3% GO:0048704 embryonic skeletal system nnorphogenesis
3% GO:0048705 skeletal system nnorphogenesis
3% GO:0048729 tissue nnorphogenesis
3% GO:0048738 cardiac muscle tissue development
3% GO:0048754 branching nnorphogenesis of a tube
3% GO:0050663 cytokine secretion
3% GO:0050671 positive regulation of lymphocyte proliferation
3% GO:0050680 negative regulation of epithelial cell proliferation
3% GO:0050728 negative regulation of inflammatory response
3% GO:0050766 positive regulation of phagocytosis
3% GO:0050767 regulation of neurogenesis
3% GO:0050770 regulation of axonogenesis
3% GO:0050806 positive regulation of synaptic transmission
3% GO:0050808 synapse organization
3% GO:0050830 defense response to Gram-positive bacterium
3% GO:0050854 regulation of antigen receptor-mediated signaling
pathway
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3% GO:0050866 negative regulation of cell activation
3% GO:0050890 cognition
3% GO:0050922 negative regulation of chennotaxis
3% GO:0050926 regulation of positive chennotaxis
3% GO:0051055 negative regulation of lipid biosynthetic process
3% GO:0051129 negative regulation of cellular component
organization
3% GO:0051130 positive regulation of cellular component
organization
3% GO:0051174 regulation of phosphorus metabolic process
3% GO:0051241 negative regulation of nnulticellular organisnnal
process
3% GO:0051271 negative regulation of cellular component movement
3% GO:0051305 chromosome movement towards spindle pole
3% GO:0051338 regulation of transferase activity
3% GO:0051387 negative regulation of nerve growth factor receptor
signaling pathway
3% GO:0051547 regulation of keratinocyte migration
3% GO:0051549 positive regulation of keratinocyte migration
3% GO:0051593 response to folic acid
3% GO:0051607 defense response to virus
3% GO:0051665 membrane raft localization
3% GO:0051716 cellular response to stimulus
3% GO:0051895 negative regulation of focal adhesion assembly
3% GO:0051896 regulation of protein kinase B signaling cascade
3% GO:0051897 positive regulation of protein kinase B signaling
cascade
3% GO:0051917 regulation of fibrinolysis
3% GO:0051928 positive regulation of calcium ion transport
3% GO:0051960 regulation of nervous system development
3% GO:0055003 cardiac myofibril assembly
3% GO:0055007 cardiac muscle cell differentiation
3% GO:0055008 cardiac muscle tissue nnorphogenesis
3% GO:0060137 maternal process involved in parturition
3% GO:0060231 nnesenchynnal to epithelial transition
3% GO:0060236 regulation of mitotic spindle organization
3% GO:0060271 cilium nnorphogenesis
3% GO:0060349 bone nnorphogenesis
3% GO:0060415 muscle tissue nnorphogenesis
3% GO:0060420 regulation of heart growth
3% GO:0060426 lung vasculature development
3% GO:0060429 epithelium development
3% GO:0060441 epithelial tube branching involved in lung
nnorphogenesis
3% GO:0060485 nnesenchynne development
3% GO:0060538 skeletal muscle organ development
3% GO:0060547 negative regulation of necrotic cell death
3% GO:0060560 developmental growth involved in nnorphogenesis
3% GO:0060562 epithelial tube nnorphogenesis
3% GO:0060606 tube closure
3% GO:0060666 dichotomous subdivision of terminal units involved in
salivary gland
branching
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3% GO:0060741 prostate gland stronnal nnorphogenesis
3% GO:0061061 muscle structure development
3% GO:0061138 nnorphogenesis of a branching epithelium
3% GO:0061318 renal filtration cell differentiation
3% GO:0070168 negative regulation of bionnineral tissue development
3% GO:0070201 regulation of establishment of protein localization
3% GO:0070206 protein trinnerization
3% GO:0070252 actin-mediated cell contraction
3% GO:0070301 cellular response to hydrogen peroxide
3% GO:0070391 response to lipoteichoic acid
3% GO:0070486 leukocyte aggregation
3% GO:0070507 regulation of nnicrotubule cytoskeleton organization
3% GO:0071214 cellular response to abiotic stimulus
3% GO:0071223 cellular response to lipoteichoic acid
3% GO:0071241 cellular response to inorganic substance
3% GO:0071260 cellular response to mechanical stimulus
3% GO:0071277 cellular response to calcium ion
3% GO:0071322 cellular response to carbohydrate stimulus
3% GO:0071347 cellular response to interleukin-1
3% GO:0071356 cellular response to tumor necrosis factor
3% GO:0071402 cellular response to lipoprotein particle stimulus
3% GO:0071453 cellular response to oxygen levels
3% GO:0071456 cellular response to hypoxia
3% GO:0071671 regulation of smooth muscle cell chennotaxis
3% GO:0071780 mitotic cell cycle G2/M transition checkpoint
3% GO:0071900 regulation of protein serine/threonine kinase
activity
3% GO:0072001 renal system development
3% GO:0072006 nephron development
3% GO:0072010 glonnerular epithelium development
3% GO:0072015 glonnerular visceral epithelial cell development
3% GO:0072102 glonnerulus nnorphogenesis
3% GO:0072109 glonnerular nnesangiunn development
3% GO:0072112 glonnerular visceral epithelial cell differentiation
3% GO:0072175 epithelial tube formation
3% GO:0072310 glonnerular epithelial cell development
3% GO:0072311 glonnerular epithelial cell differentiation
3% GO:0090023 positive regulation of neutrophil chennotaxis
3% GO:0090025 regulation of nnonocyte chennotaxis
3% GO:0090026 positive regulation of nnonocyte chennotaxis
3% GO:0090050 positive regulation of cell migration involved in
sprouting angiogenesis
3% GO:0090092 regulation of transnnennbrane receptor protein
serine/threonine kinase
signaling pathway
3% GO:0090257 regulation of muscle system process
3% GO:0097006 regulation of plasma lipoprotein particle levels
3% GO:1900048 positive regulation of hennostasis
3% GO:2000052 positive regulation of non-canonical Wnt receptor
signaling pathway
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3% GO:2000098 negative regulation of smooth muscle cell-matrix
adhesion
3% GO:2000146 negative regulation of cell motility
3% GO:2000177 regulation of neural precursor cell proliferation
3% GO:2000402 negative regulation of lymphocyte migration
3% GO:2001280 positive regulation of unsaturated fatty acid
biosynthetic process
CLAS (32 Samples)
Proportion Biological
Biological Process Name
of Samples Process
53% GO:0007399 nervous system development
38% GO:0007155 cell adhesion
38% GO:0022610 biological adhesion
38% GO:0048731 system development
38% GO:0071230 cellular response to amino acid stimulus
34% GO:0001944 vasculature development
34% GO:0022008 neurogenesis
34% GO:0030198 extracellular matrix organization
34% GO:0043062 extracellular structure organization
31% GO:0001568 blood vessel development
31% GO:0009611 response to wounding
31% GO:0030182 neuron differentiation
31% GO:0048514 blood vessel nnorphogenesis
31% GO:0048666 neuron development
31% GO:0048699 generation of neurons
31% GO:0048856 anatomical structure development
31% GO:0071346 cellular response to interferon-gamma
28% GO:0000904 cell nnorphogenesis involved in differentiation
28% GO:0006952 defense response
28% GO:0007275 nnulticellular organisnnal development
28% GO:0009607 response to biotic stimulus
28% GO:0009653 anatomical structure nnorphogenesis
28% GO:0010033 response to organic substance
28% GO:0030334 regulation of cell migration
28% GO:0031175 neuron projection development
28% GO:0032502 developmental process
28% GO:0034340 response to type I interferon
28% GO:0034341 response to interferon-gamma
28% GO:0040012 regulation of locomotion
28% GO:0048667 cell morphogenesis involved in neuron differentiation
28% GO:0048812 neuron projection nnorphogenesis
28% GO:0060333 interferon-gamma-mediated signaling pathway
28% GO:0060337 type I interferon-mediated signaling pathway
28% GO:0071229 cellular response to acid
28% GO:0071357 cellular response to type I interferon
28% GO:0072358 cardiovascular system development
28% GO:0072359 circulatory system development
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28% GO:2000145 regulation of cell motility
25% GO:0000902 cell nnorphogenesis
25% GO:0007409 axonogenesis
25% GO:0019221 cytokine-mediated signaling pathway
25% GO:0030154 cell differentiation
25% GO:0032989 cellular component nnorphogenesis
25% GO:0032990 cell part nnorphogenesis
25% GO:0034097 response to cytokine stimulus
25% GO:0040011 locomotion
25% GO:0045765 regulation of angiogenesis
25% GO:0048468 cell development
25% GO:0048858 cell projection nnorphogenesis
25% GO:0048869 cellular developmental process
25% GO:0051270 regulation of cellular component movement
25% GO:0051707 response to other organism
25% GO:0055093 response to hyperoxia
22% GO:0001101 response to acid
22% GO:0002376 immune system process
22% GO:0002504 antigen processing and presentation of peptide or
polysaccharide antigen
via MHC class ll
22% GO:0009605 response to external stimulus
22% GO:0009615 response to virus
22% GO:0010243 response to organic nitrogen
22% GO:0016477 cell migration
22% GO:0030030 cell projection organization
22% GO:0042221 response to chemical stimulus
22% GO:0043200 response to amino acid stimulus
22% GO:0048545 response to steroid hormone stimulus
22% GO:0050900 leukocyte migration
22% GO:0070482 response to oxygen levels
22% GO:0071345 cellular response to cytokine stimulus
22% GO:0071417 cellular response to organic nitrogen
22% GO:0071418 cellular response to amine stimulus
22% GO:2000147 positive regulation of cell motility
19% GO:0006935 chennotaxis
19% GO:0006955 immune response
19% GO:0007596 blood coagulation
19% GO:0007599 hennostasis
19% GO:0009612 response to mechanical stimulus
19% GO:0009888 tissue development
19% GO:0030199 collagen fibril organization
19% GO:0030335 positive regulation of cell migration
19% GO:0040017 positive regulation of locomotion
19% GO:0042060 wound healing
19% GO:0042330 taxis
19% GO:0050817 coagulation
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19% GO:0050878 regulation of body fluid levels
19% GO:0051272 positive regulation of cellular component movement
16% GO:0001525 angiogenesis
16% GO:0001822 kidney development
16% GO:0002237 response to molecule of bacterial origin
16% GO:0006950 response to stress
16% GO:0006954 inflammatory response
16% GO:0007272 ensheathnnent of neurons
16% GO:0007417 central nervous system development
16% GO:0007568 aging
16% GO:0008366 axon ensheathnnent
16% GO:0030155 regulation of cell adhesion
16% GO:0030168 platelet activation
16% GO:0032355 response to estradiol stimulus
16% GO:0032496 response to lipopolysaccharide
16% GO:0042063 gliogenesis
16% GO:0042552 nnyelination
16% GO:0045087 innate immune response
16% GO:0050793 regulation of developmental process
16% GO:0070887 cellular response to chemical stimulus
16% GO:0071310 cellular response to organic substance
13% GO:0001666 response to hypoxia
13% GO:0001775 cell activation
13% GO:0002495 antigen processing and presentation of peptide
antigen via MHC class ll
13% GO:0003008 system process
13% GO:0006928 cellular component movement
13% GO:0007162 negative regulation of cell adhesion
13% GO:0010035 response to inorganic substance
13% GO:0014075 response to amine stimulus
13% GO:0016064 innnnunoglobulin mediated immune response
13% GO:0019228 regulation of action potential in neuron
13% GO:0019886 antigen processing and presentation of exogenous
peptide antigen via
................... MHC class ll
13% GO:0022603 regulation of anatomical structure nnorphogenesis
13% GO:0032101 regulation of response to external stimulus
13% GO:0032570 response to progesterone stimulus
13% GO:0043627 response to estrogen stimulus
13% GO:0048583 regulation of response to stimulus
13% GO:0048584 positive regulation of response to stimulus
13% GO:0048870 cell motility
13% GO:0051239 regulation of nnulticellular organisnnal process
13% GO:0051674 localization of cell
13% GO:0051704 multi-organism process
13% GO:0060326 cell chennotaxis
13% GO:0060541 respiratory system development
13% GO:2000026 regulation of nnulticellular organisnnal development
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9% GO:0001505 regulation of neurotransmitter levels
9% GO:0001508 regulation of action potential
9% GO:0002250 adaptive immune response
9% GO:0002252 immune effector process
9% GO:0002253 activation of immune response
9% GO:0002443 leukocyte mediated immunity
9% GO:0002449 lymphocyte mediated immunity
9% GO:0002460 adaptive immune response based on somatic recombination
of immune
receptors built from innnnunoglobulin superfannily domains
9% GO:0002576 platelet degranulation
9% GO:0002682 regulation of immune system process
9% GO:0002684 positive regulation of immune system process
9% GO:0002768 immune response-regulating cell surface receptor
signaling pathway
9% GO:0006836 neurotransmitter transport
9% GO:0006959 hunnoral immune response
9% GO:0007267 cell-cell signaling
9% GO:0007268 synaptic transmission
9% GO:0007269 neurotransmitter secretion
9% GO:0007411 axon guidance
9% GO:0008347 glial cell migration
9% GO:0009266 response to temperature stimulus
9% GO:0009617 response to bacterium
9% GO:0009719 response to endogenous stimulus
9% GO:0014003 oligodendrocyte development
9% GO:0014013 regulation of gliogenesis
9% GO:0014047 glutamate secretion
9% GO:0014910 regulation of smooth muscle cell migration
9% GO:0016525 negative regulation of angiogenesis
9% GO:0019226 transmission of nerve impulse
9% GO:0019724 B cell mediated immunity
9% GO:0030593 neutrophil chennotaxis
9% GO:0031099 regeneration
9% GO:0032501 nnulticellular organisnnal process
9% GO:0032835 glonnerulus development
9% GO:0032879 regulation of localization
9% GO:0032964 collagen biosynthetic process
9% GO:0035637 nnulticellular organisnnal signaling
9% GO:0042391 regulation of membrane potential
9% GO:0042493 response to drug
9% GO:0044259 nnulticellular organisnnal macromolecule metabolic
process
9% GO:0045428 regulation of nitric oxide biosynthetic process
9% GO:0045766 positive regulation of angiogenesis
9% GO:0048488 synaptic vesicle endocytosis
9% GO:0048489 synaptic vesicle transport
9% GO:0048513 organ development
9% GO:0048585 negative regulation of response to stimulus
98
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9% GO:0048709 oligodendrocyte differentiation
9% GO:0050730 regulation of peptidyl-tyrosine phosphorylation
9% GO:0050776 regulation of immune response
9% GO:0050778 positive regulation of immune response
9% GO:0050804 regulation of synaptic transmission
9% GO:0050865 regulation of cell activation
9% GO:0050877 neurological system process
9% GO:0050920 regulation of chennotaxis
9% GO:0051969 regulation of transmission of nerve impulse
9% GO:0055082 cellular chemical homeostasis
9% GO:0060236 regulation of mitotic spindle organization
9% GO:0070208 protein heterotrinnerization
9% GO:0071219 cellular response to molecule of bacterial origin
9% GO:0071222 cellular response to lipopolysaccharide
9% GO:0072001 renal system development
9% GO:0072012 glonnerulus vasculature development
9% GO:0072239 nnetanephric glonnerulus vasculature development
6% GO:0000075 cell cycle checkpoint
6% GO:0000087 M phase of mitotic cell cycle
6% GO:0000236 mitotic pronnetaphase
6% GO:0000278 mitotic cell cycle
6% GO:0000279 M phase
6% GO:0000280 nuclear division
6% GO:0000302 response to reactive oxygen species
6% GO:0001501 skeletal system development
6% GO:0001504 neurotransmitter uptake
6% GO:0001817 regulation of cytokine production
6% GO:0002429 immune response-activating cell surface receptor
signaling pathway
6% GO:0002455 hunnoral immune response mediated by circulating
innnnunoglobulin
6% GO:0002520 immune system development
6% GO:0002521 leukocyte differentiation
6% GO:0002544 chronic inflammatory response
6% GO:0002675 positive regulation of acute inflammatory response
6% GO:0002683 negative regulation of immune system process
6% GO:0002685 regulation of leukocyte migration
6% GO:0002690 positive regulation of leukocyte chennotaxis
6% GO:0002694 regulation of leukocyte activation
6% GO:0003001 generation of a signal involved in cell-cell
signaling
6% GO:0006260 DNA replication
6% GO:0006693 prostaglandin metabolic process
6% GO:0006873 cellular ion homeostasis
6% GO:0006909 phagocytosis
6% GO:0006916 anti-apoptosis
6% GO:0006956 complement activation
6% GO:0006958 complement activation, classical pathway
6% GO:0007067 mitosis
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6% GO:0007160 cell-matrix adhesion
6% GO:0007166 cell surface receptor signaling pathway
6% GO:0007416 synapse assembly
6% GO:0008284 positive regulation of cell proliferation
6% GO:0008285 negative regulation of cell proliferation
6% GO:0009628 response to abiotic stimulus
6% GO:0009887 organ nnorphogenesis
6% GO:0010001 glial cell differentiation
6% GO:0010564 regulation of cell cycle process
6% GO:0010646 regulation of cell communication
6% GO:0010647 positive regulation of cell communication
6% GO:0010812 negative regulation of cell-substrate adhesion
6% GO:0014014 negative regulation of gliogenesis
6% GO:0014070 response to organic cyclic compound
6% GO:0016337 cell-cell adhesion
6% GO:0019229 regulation of vasoconstriction
6% GO:0019882 antigen processing and presentation
6% GO:0022402 cell cycle process
6% GO:0022403 cell cycle phase
6% GO:0023051 regulation of signaling
6% GO:0023052 signaling
6% GO:0023056 positive regulation of signaling
6% GO:0023061 signal release
6% GO:0030097 hennopoiesis
6% GO:0030098 lymphocyte differentiation
6% GO:0030595 leukocyte chennotaxis
6% GO:0031102 neuron projection regeneration
6% GO:0031294 lymphocyte costinnulation
6% GO:0031295 T cell costinnulation
6% GO:0031589 cell-substrate adhesion
6% GO:0031644 regulation of neurological system process
6% GO:0031663 lipopolysaccharide-mediated signaling pathway
6% GO:0031960 response to corticosteroid stimulus
6% GO:0032103 positive regulation of response to external stimulus
6% GO:0032940 secretion by cell
6% GO:0035295 tube development
6% GO:0035457 cellular response to interferon-alpha
6% GO:0035924 cellular response to vascular endothelial growth
factor stimulus
6% GO:0042127 regulation of cell proliferation
6% GO:0042476 odontogenesis
6% GO:0043086 negative regulation of catalytic activity
6% GO:0044057 regulation of system process
6% GO:0044236 nnulticellular organisnnal metabolic process
6% GO:0045321 leukocyte activation
6% GO:0045429 positive regulation of nitric oxide biosynthetic
process
6% GO:0046903 secretion
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6% GO:0048010 vascular endothelial growth factor receptor signaling
pathway
6% GO:0048167 regulation of synaptic plasticity
6% GO:0048285 organelle fission
6% GO:0048519 negative regulation of biological process
6% GO:0048520 positive regulation of behavior
6% GO:0048706 embryonic skeletal system development
6% GO:0050727 regulation of inflammatory response
6% GO:0050729 positive regulation of inflammatory response
6% GO:0050732 negative regulation of peptidyl-tyrosine
phosphorylation
6% GO:0050795 regulation of behavior
6% GO:0050808 synapse organization
6% GO:0050851 antigen receptor-mediated signaling pathway
6% GO:0050867 positive regulation of cell activation
6% GO:0050870 positive regulation of T cell activation
6% GO:0050896 response to stimulus
6% GO:0050921 positive regulation of chennotaxis
6% GO:0051050 positive regulation of transport
6% GO:0051384 response to glucocorticoid stimulus
6% GO:0052547 regulation of peptidase activity
6% GO:0060627 regulation of vesicle-mediated transport
6% GO:0061041 regulation of wound healing
6% GO:0061298 retina vasculature development in camera-type eye
6% GO:0070372 regulation of ERK1 and ERK2 cascade
6% GO:0071156 regulation of cell cycle arrest
6% GO:0071216 cellular response to biotic stimulus
6% GO:0072006 nephron development
6% GO:0072224 nnetanephric glonnerulus development
6% GO:0072376 protein activation cascade
6% GO:0080134 regulation of response to stress
6% GO:2000097 regulation of smooth muscle cell-matrix adhesion
3% GO:0000070 mitotic sister chromatid segregation
3% GO:0000082 G1/S transition of mitotic cell cycle
3% GO:0000226 nnicrotubule cytoskeleton organization
3% GO:0000819 sister chromatid segregation
3% GO:0001655 urogenital system development
3% GO:0001656 nnetanephros development
3% GO:0001736 establishment of planar polarity
3% GO:0001796 regulation of type Ila hypersensitivity
3% GO:0001798 positive regulation of type Ila hypersensitivity
3% GO:0001889 liver development
3% GO:0001893 maternal placenta development
3% GO:0001915 negative regulation of T cell mediated cytotoxicity
3% GO:0001933 negative regulation of protein phosphorylation
3% GO:0002011 nnorphogenesis of an epithelial sheet
3% GO:0002138 retinoic acid biosynthetic process
3% GO:0002175 protein localization to paranode region of axon
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3% GO:0002246 wound healing involved in inflammatory response
3% GO:0002274 myeloid leukocyte activation
3% GO:0002474 antigen processing and presentation of peptide antigen
via MHC class I
3% GO:0002478 antigen processing and presentation of exogenous
peptide antigen
3% GO:0002479 antigen processing and presentation of exogenous
peptide antigen via
................... MHC class I, TAP-dependent
3% GO:0002480 antigen processing and presentation of exogenous
peptide antigen via
MHC class I, TAP-independent
3% GO:0002507 tolerance induction
3% GO:0002526 acute inflammatory response
3% GO:0002673 regulation of acute inflammatory response
3% GO:0002687 positive regulation of leukocyte migration
3% GO:0002688 regulation of leukocyte chennotaxis
3% GO:0002697 regulation of immune effector process
3% GO:0002698 negative regulation of immune effector process
3% GO:0002699 positive regulation of immune effector process
3% GO:0002703 regulation of leukocyte mediated immunity
3% GO:0002706 regulation of lymphocyte mediated immunity
3% GO:0002709 regulation of T cell mediated immunity
3% GO:0002718 regulation of cytokine production involved in immune
response
3% GO:0002757 immune response-activating signal transduction
3% GO:0002764 immune response-regulating signaling pathway
3% GO:0002765 immune response-inhibiting signal transduction
3% GO:0002767 immune response-inhibiting cell surface receptor
signaling pathway
3% GO:0002774 Fc receptor mediated inhibitory signaling pathway
3% GO:0002819 regulation of adaptive immune response
3% GO:0002820 negative regulation of adaptive immune response
3% GO:0002822 regulation of adaptive immune response based on
somatic recombination
of immune receptors built from innnnunoglobulin superfannily domains
3% GO:0002888 positive regulation of myeloid leukocyte mediated
immunity
3% GO:0002889 regulation of innnnunoglobulin mediated immune
response
3% GO:0002892 regulation of type ll hypersensitivity
3% GO:0002894 positive regulation of type ll hypersensitivity
3% GO:0003002 regionalization
3% GO:0003013 circulatory system process
3% GO:0003094 glonnerular filtration
3% GO:0003149 membranous septum nnorphogenesis
3% GO:0003150 muscular septum nnorphogenesis
3% GO:0003281 ventricular septum development
3% GO:0006259 DNA metabolic process
3% GO:0006261 DNA-dependent DNA replication
3% GO:0006270 DNA-dependent DNA replication initiation
3% GO:0006271 DNA strand elongation involved in DNA replication
3% GO:0006281 DNA repair
3% GO:0006323 DNA packaging
3% GO:0006333 chromatin assembly or disassembly
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3% GO:0006334 nucleosonne assembly
3% GO:0006336 DNA replication-independent nucleosonne assembly
3% GO:0006692 prostanoid metabolic process
3% GO:0006811 ion transport
3% GO:0006812 cation transport
3% GO:0006814 sodium ion transport
3% GO:0006821 chloride transport
3% GO:0006826 iron ion transport
3% GO:0006879 cellular iron ion homeostasis
3% GO:0006887 exocytosis
3% GO:0006996 organelle organization
3% GO:0007010 cytoskeleton organization
3% GO:0007017 nnicrotubule-based process
3% GO:0007018 nnicrotubule-based movement
3% GO:0007049 cell cycle
3% GO:0007051 spindle organization
3% GO:0007059 chromosome segregation
3% GO:0007076 mitotic chromosome condensation
3% GO:0007093 mitotic cell cycle checkpoint
3% GO:0007094 mitotic cell cycle spindle assembly checkpoint
3% GO:0007156 honnophilic cell adhesion
3% GO:0007159 leukocyte cell-cell adhesion
3% GO:0007164 establishment of tissue polarity
3% GO:0007165 signal transduction
3% GO:0007179 transforming growth factor beta receptor signaling
pathway
3% GO:0007194 negative regulation of adenylate cyclase activity
3% GO:0007199 G-protein signaling, coupled to cGMP nucleotide
second messenger
3% GO:0007214 gamma-anninobutyric acid signaling pathway
3% GO:0007229 integrin-mediated signaling pathway
3% GO:0007346 regulation of mitotic cell cycle
3% GO:0007420 brain development
3% GO:0007431 salivary gland development
3% GO:0007517 muscle organ development
3% GO:0007610 behavior
3% GO:0007611 learning or memory
3% GO:0007612 learning
3% GO:0007613 memory
3% GO:0008015 blood circulation
3% GO:0008217 regulation of blood pressure
3% GO:0008360 regulation of cell shape
3% GO:0008406 gonad development
3% GO:0009221 pyrinnidine deoxyribonucleotide biosynthetic process
3% GO:0009263 deoxyribonucleotide biosynthetic process
3% GO:0009306 protein secretion
3% GO:0009725 response to hormone stimulus
3% GO:0009743 response to carbohydrate stimulus
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3% GO:0009746 response to hexose stimulus
3% GO:0009749 response to glucose stimulus
3% GO:0009792 embryo development ending in birth or egg hatching
3% GO:0009952 anterior/posterior pattern specification
3% GO:0009954 proximal/distal pattern formation
3% GO:0009967 positive regulation of signal transduction
3% GO:0010038 response to metal ion
3% GO:0010332 response to gamma radiation
3% GO:0010466 negative regulation of peptidase activity
3% GO:0010563 negative regulation of phosphorus metabolic process
3% GO:0010574 regulation of vascular endothelial growth factor
production
3% GO:0010648 negative regulation of cell communication
3% GO:0010716 negative regulation of extracellular matrix
disassembly
3% GO:0010718 positive regulation of epithelial to nnesenchynnal
transition
3% GO:0010720 positive regulation of cell development
3% GO:0010721 negative regulation of cell development
3% GO:0010758 regulation of macrophage chennotaxis
3% GO:0010759 positive regulation of macrophage chennotaxis
3% GO:0010810 regulation of cell-substrate adhesion
3% GO:0010811 positive regulation of cell-substrate adhesion
3% GO:0010935 regulation of macrophage cytokine production
3% GO:0010936 negative regulation of macrophage cytokine production
3% GO:0010941 regulation of cell death
3% GO:0010951 negative regulation of endopeptidase activity
3% GO:0010955 negative regulation of protein processing
3% GO:0014015 positive regulation of gliogenesis
3% GO:0014706 striated muscle tissue development
3% GO:0014805 smooth muscle adaptation
3% GO:0015672 monovalent inorganic cation transport
3% GO:0015698 inorganic anion transport
3% GO:0015807 L-amino acid transport
3% GO:0016043 cellular component organization
3% GO:0016048 detection of temperature stimulus
3% GO:0016079 synaptic vesicle exocytosis
3% GO:0016188 synaptic vesicle maturation
3% GO:0016339 calcium-dependent cell-cell adhesion
3% GO:0018149 peptide cross-linking
3% GO:0019725 cellular homeostasis
3% GO:0019884 antigen processing and presentation of exogenous
antigen
3% GO:0021529 spinal cord oligodendrocyte cell differentiation
3% GO:0021530 spinal cord oligodendrocyte cell fate specification
3% GO:0021537 telencephalon development
3% GO:0021543 palliunn development
3% GO:0021778 oligodendrocyte cell fate specification
3% GO:0021780 glial cell fate specification
3% GO:0021782 glial cell development
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3% GO:0021882 regulation of transcription from RNA polynnerase II
promoter involved in
forebrain neuron fate commitment
3% GO:0021893 cerebral cortex GABAergic interneuron fate commitment
3% GO:0021953 central nervous system neuron differentiation
3% GO:0021954 central nervous system neuron development
3% GO:0022010 central nervous system nnyelination
3% GO:0022406 membrane docking
3% GO:0022409 positive regulation of cell-cell adhesion
3% GO:0022602 ovulation cycle process
3% GO:0022604 regulation of cell nnorphogenesis
3% GO:0022614 membrane to membrane docking
3% GO:0022616 DNA strand elongation
3% GO:0023057 negative regulation of signaling
3% GO:0030001 metal ion transport
3% GO:0030036 actin cytoskeleton organization
3% GO:0030071 regulation of mitotic metaphase/anaphase transition
3% GO:0030100 regulation of endocytosis
3% GO:0030111 regulation of Wnt receptor signaling pathway
3% GO:0030217 T cell differentiation
3% GO:0030261 chromosome condensation
3% GO:0030323 respiratory tube development
3% GO:0030324 lung development
3% GO:0030800 negative regulation of cyclic nucleotide metabolic
process
3% GO:0030803 negative regulation of cyclic nucleotide biosynthetic
process
3% GO:0030809 negative regulation of nucleotide biosynthetic process
3% GO:0030815 negative regulation of cAMP metabolic process
3% GO:0030818 negative regulation of cAMP biosynthetic process
3% GO:0031055 chromatin remodeling at centronnere
3% GO:0031100 organ regeneration
3% GO:0031280 negative regulation of cyclase activity
3% GO:0031344 regulation of cell projection organization
3% GO:0031347 regulation of defense response
3% GO:0031497 chromatin assembly
3% GO:0031577 spindle checkpoint
3% GO:0031646 positive regulation of neurological system process
3% GO:0032091 negative regulation of protein binding
3% GO:0032228 regulation of synaptic transmission, GABAergic
3% GO:0032291 axon ensheathnnent in central nervous system
3% GO:0032680 regulation of tumor necrosis factor production
3% GO:0032763 regulation of mast cell cytokine production
3% GO:0032944 regulation of mononuclear cell proliferation
3% GO:0032963 collagen metabolic process
3% GO:0033003 regulation of mast cell activation
3% GO:0034080 CenH3-containing nucleosonne assembly at centronnere
3% GO:0034220 ion transnnennbrane transport
3% GO:0034284 response to nnonosaccharide stimulus
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3% GO:0034447 very-low-density lipoprotein particle clearance
3% GO:0034508 centronnere complex assembly
3% GO:0034612 response to tumor necrosis factor
3% GO:0034724 DNA replication-independent nucleosonne organization
3% GO:0034728 nucleosonne organization
3% GO:0035239 tube nnorphogenesis
3% GO:0035567 non-canonical Wnt receptor signaling pathway
3% GO:0035850 epithelial cell differentiation involved in kidney
development
3% GO:0042129 regulation of T cell proliferation
3% GO:0042312 regulation of vasodilation
3% GO:0042326 negative regulation of phosphorylation
3% GO:0042554 superoxide anion generation
3% GO:0042590 antigen processing and presentation of exogenous
peptide antigen via
................... MHC class I
3% GO:0042592 homeostatic process
3% GO:0042742 defense response to bacterium
3% GO:0042981 regulation of apoptotic process
3% GO:0043009 chordate embryonic development
3% GO:0043044 ATP-dependent chromatin remodeling
3% GO:0043066 negative regulation of apoptotic process
3% GO:0043069 negative regulation of programmed cell death
3% GO:0043092 L-amino acid import
3% GO:0043299 leukocyte degranulation
3% GO:0043368 positive T cell selection
3% GO:0043393 regulation of protein binding
3% GO:0043405 regulation of MAP kinase activity
3% GO:0043408 regulation of MAPK cascade
3% GO:0043486 histone exchange
3% GO:0043550 regulation of lipid kinase activity
3% GO:0043552 positive regulation of phosphatidylinositol 3-kinase
activity
3% GO:0043584 nose development
3% GO:0043588 skin development
3% GO:0044092 negative regulation of molecular function
3% GO:0044246 regulation of nnulticellular organisnnal metabolic
process
3% GO:0045058 T cell selection
3% GO:0045059 positive thymic T cell selection
3% GO:0045061 thymic T cell selection
3% GO:0045137 development of primary sexual characteristics
3% GO:0045596 negative regulation of cell differentiation
3% GO:0045664 regulation of neuron differentiation
3% GO:0045665 negative regulation of neuron differentiation
3% GO:0045685 regulation of glial cell differentiation
3% GO:0045686 negative regulation of glial cell differentiation
3% GO:0045787 positive regulation of cell cycle
3% GO:0045839 negative regulation of mitosis
3% GO:0045841 negative regulation of mitotic metaphase/anaphase
transition
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3% GO:0045907 positive regulation of vasoconstriction
3% GO:0045909 positive regulation of vasodilation
3% GO:0045936 negative regulation of phosphate metabolic process
3% GO:0045980 negative regulation of nucleotide metabolic process
3% GO:0046697 decidualization
3% GO:0048002 antigen processing and presentation of peptide
antigen
3% GO:0048008 platelet-derived growth factor receptor signaling
pathway
3% GO:0048168 regulation of neuronal synaptic plasticity
3% GO:0048523 negative regulation of cellular process
3% GO:0048534 hennopoietic or lymphoid organ development
3% GO:0048568 embryonic organ development
3% GO:0048608 reproductive structure development
3% GO:0048646 anatomical structure formation involved in
nnorphogenesis
3% GO:0048660 regulation of smooth muscle cell proliferation
3% GO:0048661 positive regulation of smooth muscle cell
proliferation
3% GO:0048663 neuron fate commitment
3% GO:0048676 axon extension involved in development
3% GO:0048678 response to axon injury
3% GO:0048704 embryonic skeletal system nnorphogenesis
3% GO:0048705 skeletal system nnorphogenesis
3% GO:0048713 regulation of oligodendrocyte differentiation
3% GO:0048715 negative regulation of oligodendrocyte differentiation
3% GO:0048736 appendage development
3% GO:0048741 skeletal muscle fiber development
3% GO:0048771 tissue remodeling
3% GO:0048872 homeostasis of number of cells
3% GO:0048878 chemical homeostasis
3% GO:0050000 chromosome localization
3% GO:0050663 cytokine secretion
3% GO:0050665 hydrogen peroxide biosynthetic process
3% GO:0050670 regulation of lymphocyte proliferation
3% GO:0050767 regulation of neurogenesis
3% GO:0050777 negative regulation of immune response
3% GO:0050801 ion homeostasis
3% GO:0050806 positive regulation of synaptic transmission
3% GO:0050852 T cell receptor signaling pathway
3% GO:0050864 regulation of B cell activation
3% GO:0050890 cognition
3% GO:0050922 negative regulation of chennotaxis
3% GO:0050926 regulation of positive chennotaxis
3% GO:0050927 positive regulation of positive chennotaxis
3% GO:0051049 regulation of transport
3% GO:0051093 negative regulation of developmental process
3% GO:0051094 positive regulation of developmental process
3% GO:0051098 regulation of binding
3% GO:0051100 negative regulation of binding
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3% GO:0051128 regulation of cellular component organization
3% GO:0051216 cartilage development
3% GO:0051240 positive regulation of nnulticellular organisnnal
process
3% GO:0051241 negative regulation of nnulticellular organisnnal
process
3% GO:0051249 regulation of lymphocyte activation
3% GO:0051276 chromosome organization
3% GO:0051301 cell division
3% GO:0051303 establishment of chromosome localization
3% GO:0051325 interphase
3% GO:0051329 interphase of mitotic cell cycle
3% GO:0051346 negative regulation of hydrolase activity
3% GO:0051350 negative regulation of lyase activity
3% GO:0051383 kinetochore organization
3% GO:0051482 elevation of cytosolic calcium ion concentration
involved in G-protein
................... signaling coupled to IP3 second messenger
3% GO:0051668 localization within membrane
3% GO:0051716 cellular response to stimulus
3% GO:0051726 regulation of cell cycle
3% GO:0051782 negative regulation of cell division
3% GO:0051784 negative regulation of nuclear division
3% GO:0051960 regulation of nervous system development
3% GO:0051971 positive regulation of transmission of nerve impulse
3% GO:0051983 regulation of chromosome segregation
3% GO:0055002 striated muscle cell development
3% GO:0055072 iron ion homeostasis
3% GO:0055085 transnnennbrane transport
3% GO:0060071 Wnt receptor signaling pathway, planar cell polarity
pathway
3% GO:0060173 limb development
3% GO:0060348 bone development
3% GO:0060412 ventricular septum nnorphogenesis
3% GO:0060441 epithelial tube branching involved in lung
nnorphogenesis
3% GO:0060537 muscle tissue development
3% GO:0060548 negative regulation of cell death
3% GO:0060712 spongiotrophoblast layer development
3% GO:0061008 hepaticobiliary system development
3% GO:0061061 muscle structure development
3% GO:0061138 nnorphogenesis of a branching epithelium
3% GO:0061318 renal filtration cell differentiation
3% GO:0061351 neural precursor cell proliferation
3% GO:0065004 protein-DNA complex assembly
3% GO:0065008 regulation of biological quality
3% GO:0070374 positive regulation of ERK1 and ERK2 cascade
3% GO:0070555 response to interleukin-1
3% GO:0070613 regulation of protein processing
3% GO:0070663 regulation of leukocyte proliferation
3% GO:0070664 negative regulation of leukocyte proliferation
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3% GO:0071103 DNA conformation change
3% GO:0071173 spindle assembly checkpoint
3% GO:0071174 mitotic cell cycle spindle checkpoint
3% GO:0071248 cellular response to metal ion
3% GO:0071260 cellular response to mechanical stimulus
3% GO:0071276 cellular response to cadmium ion
3% GO:0071277 cellular response to calcium ion
3% GO:0071347 cellular response to interleukin-1
3% GO:0071356 cellular response to tumor necrosis factor
3% GO:0071455 cellular response to hyperoxia
3% GO:0071637 regulation of nnonocyte chennotactic protein-1
production
3% GO:0071675 regulation of mononuclear cell migration
3% GO:0071824 protein-DNA complex subunit organization
3% GO:0071840 cellular component organization or biogenesis
3% GO:0071841 cellular component organization or biogenesis at
cellular level
3% GO:0071842 cellular component organization at cellular level
3% GO:0072010 glonnerular epithelium development
3% GO:0072109 glonnerular nnesangiunn development
3% GO:0072110 glonnerular nnesangial cell proliferation
3% GO:0072112 glonnerular visceral epithelial cell differentiation
3% GO:0072311 glonnerular epithelial cell differentiation
3% GO:0090025 regulation of nnonocyte chennotaxis
3% GO:0090049 regulation of cell migration involved in sprouting
angiogenesis
3% GO:0090175 regulation of establishment of planar polarity
3% GO:0090224 regulation of spindle organization
3% GO:0097205 renal filtration
3% GO:2000300 regulation of synaptic vesicle exocytosis
3% GO:2000401 regulation of lymphocyte migration
3% GO:2000402 negative regulation of lymphocyte migration
3% GO:2000501 regulation of natural killer cell chennotaxis
SL (20 Samples)
Proportion Biological
Biological Process Name
of Samples Process
80% GO:0007399 nervous system development
55% GO:0022008 neurogenesis
50% GO:0048699 generation of neurons
40% GO:0002504 antigen processing and presentation of peptide or
polysaccharide antigen
via MHC class ll
40% GO:0042063 gliogenesis
35% GO:0030182 neuron differentiation
35% GO:0048468 cell development
30% GO:0007417 central nervous system development
30% GO:0048167 regulation of synaptic plasticity
30% GO:0048731 system development
30% GO:0048856 anatomical structure development
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30% GO:0050793 regulation of developmental process
25% GO:0001568 blood vessel development
25% GO:0010001 glial cell differentiation
25% GO:0010033 response to organic substance
25% GO:0031960 response to corticosteroid stimulus
25% GO:0034341 response to interferon-gamma
25% GO:0051384 response to glucocorticoid stimulus
25% GO:0060333 interferon-gamma-mediated signaling pathway
25% GO:0071229 cellular response to acid
25% GO:0071346 cellular response to interferon-gamma
20% GO:0001101 response to acid
20% GO:0001944 vasculature development
20% GO:0002495 antigen processing and presentation of peptide
antigen via MHC class ll
20% GO:0006952 defense response
20% GO:0007267 cell-cell signaling
20% GO:0007268 synaptic transmission
20% GO:0007269 neurotransmitter secretion
20% GO:0007275 nnulticellular organisnnal development
20% GO:0010243 response to organic nitrogen
20% GO:0014013 regulation of gliogenesis
20% GO:0014047 glutamate secretion
20% GO:0019226 transmission of nerve impulse
20% GO:0019886 antigen processing and presentation of exogenous
peptide antigen via
................... MHC class ll
20% GO:0031644 regulation of neurological system process
20% GO:0032940 secretion by cell
20% GO:0035295 tube development
20% GO:0035637 nnulticellular organisnnal signaling
20% GO:0048168 regulation of neuronal synaptic plasticity
20% GO:0048489 synaptic vesicle transport
20% GO:0048709 oligodendrocyte differentiation
20% GO:0050767 regulation of neurogenesis
20% GO:0050804 regulation of synaptic transmission
20% GO:0050877 neurological system process
20% GO:0051093 negative regulation of developmental process
20% GO:0051960 regulation of nervous system development
20% GO:0051969 regulation of transmission of nerve impulse
20% GO:2000026 regulation of nnulticellular organisnnal development
15% GO:0000904 cell nnorphogenesis involved in differentiation
15% GO:0001505 regulation of neurotransmitter levels
15% GO:0001822 kidney development
15% GO:0003001 generation of a signal involved in cell-cell
signaling
15% GO:0003008 system process
15% GO:0006836 neurotransmitter transport
15% GO:0007155 cell adhesion
15% GO:0007409 axonogenesis
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15% GO:0008284 positive regulation of cell proliferation
15% GO:0009611 response to wounding
15% GO:0009653 anatomical structure nnorphogenesis
15% GO:0016064 innnnunoglobulin mediated immune response
15% GO:0019228 regulation of action potential in neuron
15% GO:0019724 B cell mediated immunity
15% GO:0022603 regulation of anatomical structure nnorphogenesis
15% GO:0022610 biological adhesion
15% GO:0023061 signal release
15% GO:0030030 cell projection organization
15% GO:0030154 cell differentiation
15% GO:0030323 respiratory tube development
15% GO:0030324 lung development
15% GO:0031175 neuron projection development
15% GO:0034097 response to cytokine stimulus
15% GO:0035239 tube nnorphogenesis
15% GO:0042127 regulation of cell proliferation
15% GO:0042221 response to chemical stimulus
15% GO:0043066 negative regulation of apoptotic process
15% GO:0043069 negative regulation of programmed cell death
15% GO:0043200 response to amino acid stimulus
15% GO:0044057 regulation of system process
15% GO:0045595 regulation of cell differentiation
15% GO:0045596 negative regulation of cell differentiation
15% GO:0045915 positive regulation of catecholannine metabolic
process
15% GO:0045964 positive regulation of dopamine metabolic process
15% GO:0048666 neuron development
15% GO:0048667 cell nnorphogenesis involved in neuron
differentiation
15% GO:0048712 negative regulation of astrocyte differentiation
15% GO:0048812 neuron projection nnorphogenesis
15% GO:0048869 cellular developmental process
15% GO:0050890 cognition
15% GO:0051239 regulation of nnulticellular organisnnal process
15% GO:0060541 respiratory system development
15% GO:0072001 renal system development
10% GO:0000902 cell nnorphogenesis
10% GO:0001838 embryonic epithelial tube formation
10% GO:0002250 adaptive immune response
10% GO:0002252 immune effector process
10% GO:0002376 immune system process
10% GO:0002443 leukocyte mediated immunity
10% GO:0002449 lymphocyte mediated immunity
10% GO:0002460 adaptive immune response based on somatic recombination
of immune
receptors built from innnnunoglobulin superfannily domains
10% GO:0002682 regulation of immune system process
10% GO:0002684 positive regulation of immune system process
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10% GO:0006887 exocytosis
10% GO:0006955 immune response
10% GO:0006956 complement activation
10% GO:0006959 hunnoral immune response
10% GO:0007214 gamma-anninobutyric acid signaling pathway
10% GO:0007219 Notch signaling pathway
10% GO:0007272 ensheathnnent of neurons
10% GO:0007610 behavior
10% GO:0007611 learning or memory
10% GO:0008366 axon ensheathnnent
10% GO:0009719 response to endogenous stimulus
10% GO:0014075 response to amine stimulus
10% GO:0016477 cell migration
10% GO:0019221 cytokine-mediated signaling pathway
10% GO:0019827 stem cell maintenance
10% GO:0021778 oligodendrocyte cell fate specification
10% GO:0021780 glial cell fate specification
10% GO:0021781 glial cell fate commitment
10% GO:0030168 platelet activation
10% GO:0030199 collagen fibril organization
10% GO:0030334 regulation of cell migration
10% GO:0030595 leukocyte chennotaxis
10% GO:0032101 regulation of response to external stimulus
10% GO:0032501 nnulticellular organisnnal process
10% GO:0032989 cellular component nnorphogenesis
10% GO:0032990 cell part nnorphogenesis
10% GO:0034340 response to type I interferon
10% GO:0035019 somatic stem cell maintenance
10% GO:0035148 tube formation
10% GO:0040011 locomotion
10% GO:0042391 regulation of membrane potential
10% GO:0042552 nnyelination
10% GO:0045087 innate immune response
10% GO:0045664 regulation of neuron differentiation
10% GO:0045665 negative regulation of neuron differentiation
10% GO:0046903 secretion
10% GO:0048488 synaptic vesicle endocytosis
10% GO:0048514 blood vessel nnorphogenesis
10% GO:0048545 response to steroid hormone stimulus
10% GO:0048583 regulation of response to stimulus
10% GO:0048584 positive regulation of response to stimulus
10% GO:0048729 tissue nnorphogenesis
10% GO:0048858 cell projection nnorphogenesis
10% GO:0048864 stem cell development
10% GO:0048870 cell motility
10% GO:0050806 positive regulation of synaptic transmission
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10% GO:0050900 leukocyte migration
10% GO:0050920 regulation of chennotaxis
10% GO:0051050 positive regulation of transport
10% GO:0051674 localization of cell
10% GO:0060284 regulation of cell development
10% GO:0060326 cell chennotaxis
10% GO:0060337 type I interferon-mediated signaling pathway
10% GO:0060548 negative regulation of cell death
10% GO:0060562 epithelial tube nnorphogenesis
10% GO:0060627 regulation of vesicle-mediated transport
10% GO:0071357 cellular response to type I interferon
10% GO:0072070 loop of Henle development
10% GO:0072175 epithelial tube formation
5% GO:0000302 response to reactive oxygen species
5% GO:0001504 neurotransmitter uptake
5% GO:0001655 urogenital system development
5% GO:0001656 nnetanephros development
5% GO:0001738 nnorphogenesis of a polarized epithelium
5% GO:0001796 regulation of type Ila hypersensitivity
5% GO:0001798 positive regulation of type Ila hypersensitivity
5% GO:0001843 neural tube closure
5% GO:0002009 nnorphogenesis of an epithelium
5% GO:0002053 positive regulation of nnesenchynnal cell
proliferation
5% GO:0002237 response to molecule of bacterial origin
5% GO:0002253 activation of immune response
5% GO:0002274 myeloid leukocyte activation
5% GO:0002282 nnicroglial cell activation involved in immune
response
5% GO:0002429 immune response-activating cell surface receptor
signaling pathway
5% GO:0002431 Fc receptor mediated stimulatory signaling pathway
5% GO:0002455 hunnoral immune response mediated by circulating
innnnunoglobulin
5% GO:0002507 tolerance induction
5% GO:0002576 platelet degranulation
5% GO:0002685 regulation of leukocyte migration
5% GO:0002687 positive regulation of leukocyte migration
5% GO:0002688 regulation of leukocyte chennotaxis
5% GO:0002690 positive regulation of leukocyte chennotaxis
5% GO:0002694 regulation of leukocyte activation
5% GO:0002696 positive regulation of leukocyte activation
5% GO:0002757 immune response-activating signal transduction
5% GO:0002764 immune response-regulating signaling pathway
5% GO:0002768 immune response-regulating cell surface receptor
signaling pathway
5% GO:0002886 regulation of myeloid leukocyte mediated immunity
5% GO:0002888 positive regulation of myeloid leukocyte mediated
immunity
5% GO:0002892 regulation of type ll hypersensitivity
5% GO:0002894 positive regulation of type ll hypersensitivity
5% GO:0003094 glonnerular filtration
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5% GO:0006119 oxidative phosphorylation
5% GO:0006120 mitochondrial electron transport, NADH to ubiquinone
5% GO:0006821 chloride transport
5% GO:0006928 cellular component movement
5% GO:0006935 chennotaxis
5% GO:0006954 inflammatory response
5% GO:0006958 complement activation, classical pathway
5% GO:0007160 cell-matrix adhesion
5% GO:0007263 nitric oxide mediated signal transduction
5% GO:0007568 aging
5% GO:0007584 response to nutrient
5% GO:0007596 blood coagulation
5% GO:0007599 hennostasis
5% GO:0007612 learning
5% GO:0007626 loconnotory behavior
5% GO:0008347 glial cell migration
5% GO:0009124 nucleoside nnonophosphate biosynthetic process
5% GO:0009605 response to external stimulus
5% GO:0009612 response to mechanical stimulus
5% GO:0009888 tissue development
5% GO:0009967 positive regulation of signal transduction
5% GO:0009991 response to extracellular stimulus
5% GO:0010035 response to inorganic substance
5% GO:0010212 response to ionizing radiation
5% GO:0010332 response to gamma radiation
5% GO:0010563 negative regulation of phosphorus metabolic process
5% GO:0010574 regulation of vascular endothelial growth factor
production
5% GO:0010575 positive regulation vascular endothelial growth
factor production
5% GO:0010621 negative regulation of transcription by transcription
factor localization
5% GO:0010646 regulation of cell communication
5% GO:0010647 positive regulation of cell communication
5% GO:0010765 positive regulation of sodium ion transport
5% GO:0010812 negative regulation of cell-substrate adhesion
5% GO:0010873 positive regulation of cholesterol esterification
5% GO:0010935 regulation of macrophage cytokine production
5% GO:0014014 negative regulation of gliogenesis
5% GO:0014015 positive regulation of gliogenesis
5% GO:0014020 primary neural tube formation
5% GO:0014032 neural crest cell development
5% GO:0014033 neural crest cell differentiation
5% GO:0015698 inorganic anion transport
5% GO:0016079 synaptic vesicle exocytosis
5% GO:0016192 vesicle-mediated transport
5% GO:0016331 nnorphogenesis of embryonic epithelium
5% GO:0016339 calcium-dependent cell-cell adhesion
5% GO:0017156 calcium ion-dependent exocytosis
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5% GO:0017157 regulation of exocytosis
5% GO:0021529 spinal cord oligodendrocyte cell differentiation
5% GO:0021530 spinal cord oligodendrocyte cell fate specification
5% GO:0021779 oligodendrocyte cell fate commitment
5% GO:0021915 neural tube development
5% GO:0021952 central nervous system projection neuron axonogenesis
5% GO:0021955 central nervous system neuron axonogenesis
5% GO:0022010 central nervous system nnyelination
5% GO:0022900 electron transport chain
5% GO:0022904 respiratory electron transport chain
5% GO:0023052 signaling
5% GO:0023056 positive regulation of signaling
5% GO:0030097 hennopoiesis
5% GO:0030155 regulation of cell adhesion
5% GO:0030198 extracellular matrix organization
5% GO:0030335 positive regulation of cell migration
5% GO:0030593 neutrophil chennotaxis
5% GO:0031099 regeneration
5% GO:0031294 lymphocyte costinnulation
5% GO:0031295 T cell costinnulation
5% GO:0031579 membrane raft organization
5% GO:0031589 cell-substrate adhesion
5% GO:0031646 positive regulation of neurological system process
5% GO:0031667 response to nutrient levels
5% GO:0032103 positive regulation of response to external stimulus
5% GO:0032291 axon ensheathnnent in central nervous system
5% GO:0032502 developmental process
5% GO:0032879 regulation of localization
5% GO:0032930 positive regulation of superoxide anion generation
5% GO:0033273 response to vitamin
5% GO:0034382 chylonnicron remnant clearance
5% GO:0035282 segmentation
5% GO:0035850 epithelial cell differentiation involved in kidney
development
5% GO:0040012 regulation of locomotion
5% GO:0040017 positive regulation of locomotion
5% GO:0042326 negative regulation of phosphorylation
5% GO:0042330 taxis
5% GO:0042493 response to drug
5% GO:0042773 ATP synthesis coupled electron transport
5% GO:0042775 mitochondria! ATP synthesis coupled electron transport
5% GO:0043062 extracellular structure organization
5% GO:0043270 positive regulation of ion transport
5% GO:0043299 leukocyte degranulation
5% GO:0045598 regulation of fat cell differentiation
5% GO:0045599 negative regulation of fat cell differentiation
5% GO:0045607 regulation of auditory receptor cell differentiation
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5% GO:0045631 regulation of nnechanoreceptor differentiation
5% GO:0045685 regulation of glial cell differentiation
5% GO:0045686 negative regulation of glial cell differentiation
5% GO:0045765 regulation of angiogenesis
5% GO:0045767 regulation of anti-apoptosis
5% GO:0045768 positive regulation of anti-apoptosis
5% GO:0045936 negative regulation of phosphate metabolic process
5% GO:0046826 negative regulation of protein export from nucleus
5% GO:0046928 regulation of neurotransmitter secretion
5% GO:0048041 focal adhesion assembly
5% GO:0048146 positive regulation of fibroblast proliferation
5% GO:0048520 positive regulation of behavior
5% GO:0048523 negative regulation of cellular process
5% GO:0048534 hennopoietic or lymphoid organ development
5% GO:0048646 anatomical structure formation involved in
nnorphogenesis
5% GO:0048710 regulation of astrocyte differentiation
5% GO:0048754 branching nnorphogenesis of a tube
5% GO:0048863 stem cell differentiation
5% GO:0050678 regulation of epithelial cell proliferation
5% GO:0050764 regulation of phagocytosis
5% GO:0050776 regulation of immune response
5% GO:0050778 positive regulation of immune response
5% GO:0050795 regulation of behavior
5% GO:0050817 coagulation
5% GO:0050851 antigen receptor-mediated signaling pathway
5% GO:0050863 regulation of T cell activation
5% GO:0050864 regulation of B cell activation
5% GO:0050865 regulation of cell activation
5% GO:0050866 negative regulation of cell activation
5% GO:0050867 positive regulation of cell activation
5% GO:0050870 positive regulation of T cell activation
5% GO:0050921 positive regulation of chennotaxis
5% GO:0050926 regulation of positive chennotaxis
5% GO:0050927 positive regulation of positive chennotaxis
5% GO:0050930 induction of positive chennotaxis
5% GO:0051049 regulation of transport
5% GO:0051249 regulation of lymphocyte activation
5% GO:0051251 positive regulation of lymphocyte activation
5% GO:0051270 regulation of cellular component movement
5% GO:0051272 positive regulation of cellular component movement
5% GO:0051414 response to cortisol stimulus
5% GO:0051823 regulation of synapse structural plasticity
5% GO:0051899 membrane depolarization
5% GO:0051971 positive regulation of transmission of nerve impulse
5% GO:0052031 modulation by synnbiont of host defense response
5% GO:0052173 response to defenses of other organism involved in
symbiotic interaction
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5% GO:0052200 response to host defenses
5% GO:0052255 modulation by organism of defense response of other
organism involved
in symbiotic interaction
5% GO:0052509 positive regulation by synnbiont of host defense
response
5% GO:0052510 positive regulation by organism of defense response of
other organism
involved in symbiotic interaction
5% GO:0052564 response to immune response of other organism involved
in symbiotic
interaction
5% GO:0052572 response to host immune response
5% GO:0060079 regulation of excitatory postsynaptic membrane
potential
5% GO:0060425 lung nnorphogenesis
5% GO:0060429 epithelium development
5% GO:0060606 tube closure
5% GO:0060688 regulation of nnorphogenesis of a branching structure
5% GO:0060696 regulation of phospholipid catabolic process
5% GO:0060697 positive regulation of phospholipid catabolic process
5% GO:0060907 positive regulation of macrophage cytokine production
5% GO:0061041 regulation of wound healing
5% GO:0061081 positive regulation of myeloid leukocyte cytokine
production involved in
................... immune response
5% GO:0065008 regulation of biological quality
5% GO:0070482 response to oxygen levels
5% GO:0070887 cellular response to chemical stimulus
5% GO:0071216 cellular response to biotic stimulus
5% GO:0071219 cellular response to molecule of bacterial origin
5% GO:0071222 cellular response to lipopolysaccharide
5% GO:0071230 cellular response to amino acid stimulus
5% GO:0071310 cellular response to organic substance
5% GO:0071345 cellular response to cytokine stimulus
5% GO:0071418 cellular response to amine stimulus
5% GO:0071470 cellular response to osmotic stress
5% GO:0071675 regulation of mononuclear cell migration
5% GO:0071830 triglyceride-rich lipoprotein particle clearance
5% GO:0072006 nephron development
5% GO:0072080 nephron tubule development
5% GO:0072358 cardiovascular system development
5% GO:0072359 circulatory system development
5% GO:0075136 response to host
5% GO:0090072 positive regulation of sodium ion transport via
voltage-gated sodium
channel activity
5% GO:0090183 regulation of kidney development
5% GO:0097205 renal filtration
5% GO:2000145 regulation of cell motility
5% GO:2000147 positive regulation of cell motility
5% GO:2000980 regulation of inner ear receptor cell differentiation
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PROLIF (31 Samples)
Proportion Biological
Biological Process Name
of Samples Process
74% GO:0000236 mitotic pronnetaphase
71% GO:0000087 M phase of mitotic cell cycle
71% GO:0000278 mitotic cell cycle
71% GO:0000280 nuclear division
71% GO:0007067 mitosis
71% GO:0048285 organelle fission
68% GO:0007059 chromosome segregation
68% GO:0022403 cell cycle phase
65% GO:0000279 M phase
65% GO:0022402 cell cycle process
61% GO:0000075 cell cycle checkpoint
61% GO:0007049 cell cycle
61% GO:0051301 cell division
58% GO:0000819 sister chromatid segregation
58% GO:0010564 regulation of cell cycle process
58% GO:0071156 regulation of cell cycle arrest
52% GO:0000070 mitotic sister chromatid segregation
52% GO:0006323 DNA packaging
52% GO:0007051 spindle organization
48% GO:0006260 DNA replication
48% GO:0006336 DNA replication-independent nucleosonne assembly
48% GO:0031577 spindle checkpoint
48% GO:0034080 CenH3-containing nucleosonne assembly at centronnere
48% GO:0034724 DNA replication-independent nucleosonne organization
48% GO:0071103 DNA conformation change
45% GO:0031055 chromatin remodeling at centronnere
45% GO:0043486 histone exchange
45% GO:0051325 interphase
45% GO:0051329 interphase of mitotic cell cycle
45% GO:0051726 regulation of cell cycle
42% GO:0006261 DNA-dependent DNA replication
42% GO:0006334 nucleosonne assembly
42% GO:0007399 nervous system development
42% GO:0031497 chromatin assembly
42% GO:0042063 gliogenesis
42% GO:0051276 chromosome organization
42% GO:0065004 protein-DNA complex assembly
39% GO:0006259 DNA metabolic process
39% GO:0006271 DNA strand elongation involved in DNA replication
39% GO:0043044 ATP-dependent chromatin remodeling
39% GO:0051983 regulation of chromosome segregation
39% GO:0071824 protein-DNA complex subunit organization
35% GO:0000226 nnicrotubule cytoskeleton organization
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35% GO:0007417 central nervous system development
35% GO:0022616 DNA strand elongation
35% GO:0034728 nucleosonne organization
32% GO:0000082 G1/S transition of mitotic cell cycle
32% GO:0006333 chromatin assembly or disassembly
32% GO:0007017 nnicrotubule-based process
32% GO:0022008 neurogenesis
32% GO:0030071 regulation of mitotic metaphase/anaphase transition
32% GO:0048709 oligodendrocyte differentiation
32% GO:0071174 mitotic cell cycle spindle checkpoint
29% GO:0007052 mitotic spindle organization
29% GO:0007093 mitotic cell cycle checkpoint
29% GO:0010001 glial cell differentiation
29% GO:0032201 telonnere maintenance via semi-conservative
replication
29% GO:0045841 negative regulation of mitotic metaphase/anaphase
transition
29% GO:0048468 cell development
29% GO:0048699 generation of neurons
26% GO:0000216 M/G1 transition of mitotic cell cycle
26% GO:0006270 DNA-dependent DNA replication initiation
26% GO:0006312 mitotic recombination
26% GO:0006996 organelle organization
26% GO:0007076 mitotic chromosome condensation
26% GO:0007094 mitotic cell cycle spindle assembly checkpoint
26% GO:0007346 regulation of mitotic cell cycle
26% GO:0021781 glial cell fate commitment
26% GO:0045664 regulation of neuron differentiation
26% GO:0048015 phosphatidylinositol-mediated signaling
26% GO:0048017 inositol lipid-mediated signaling
26% GO:0071173 spindle assembly checkpoint
23% GO:0000084 S phase of mitotic cell cycle
23% GO:0000722 telonnere maintenance via recombination
23% GO:0001944 vasculature development
23% GO:0007088 regulation of mitosis
23% GO:0007155 cell adhesion
23% GO:0022610 biological adhesion
23% GO:0030182 neuron differentiation
23% GO:0045839 negative regulation of mitosis
23% GO:0048812 neuron projection nnorphogenesis
23% GO:0050767 regulation of neurogenesis
23% GO:0050793 regulation of developmental process
23% GO:0051093 negative regulation of developmental process
23% GO:0051320 S phase
23% GO:0051783 regulation of nuclear division
23% GO:0051784 negative regulation of nuclear division
19% GO:0001568 blood vessel development
19% GO:0006281 DNA repair
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19% GO:0006974 response to DNA damage stimulus
19% GO:0014013 regulation of gliogenesis
19% GO:0030198 extracellular matrix organization
19% GO:0030261 chromosome condensation
19% GO:0043062 extracellular structure organization
19% GO:0045665 negative regulation of neuron differentiation
19% GO:0048731 system development
19% GO:0051988 regulation of attachment of spindle nnicrotubules to
kinetochore
19% GO:0060284 regulation of cell development
19% GO:0071842 cellular component organization at cellular level
19% GO:2000026 regulation of nnulticellular organisnnal development
16% GO:0002504 antigen processing and presentation of peptide or
polysaccharide antigen
................... via MHC class ll
16% GO:0006297 nucleotide-excision repair, DNA gap filling
16% GO:0006310 DNA recombination
16% GO:0006338 chromatin remodeling
16% GO:0007275 nnulticellular organisnnal development
16% GO:0010833 telonnere maintenance via telonnere lengthening
16% GO:0010948 negative regulation of cell cycle process
16% GO:0030154 cell differentiation
16% GO:0030199 collagen fibril organization
16% GO:0031145 anaphase-promoting complex-dependent proteasonnal
ubiquitin-
dependent protein catabolic process
16% GO:0048666 neuron development
16% GO:0048856 anatomical structure development
16% GO:0051383 kinetochore organization
16% GO:0071841 cellular component organization or biogenesis at
cellular level
16% GO:0072358 cardiovascular system development
16% GO:0072359 circulatory system development
13% GO:0000723 telonnere maintenance
13% GO:0000904 cell nnorphogenesis involved in differentiation
13% GO:0001101 response to acid
13% GO:0001501 skeletal system development
13% GO:0007409 axonogenesis
13% GO:0009653 anatomical structure nnorphogenesis
13% GO:0009887 organ nnorphogenesis
13% GO:0014014 negative regulation of gliogenesis
13% GO:0021529 spinal cord oligodendrocyte cell differentiation
13% GO:0021530 spinal cord oligodendrocyte cell fate specification
13% GO:0022603 regulation of anatomical structure nnorphogenesis
13% GO:0032200 telonnere organization
13% GO:0034340 response to type I interferon
13% GO:0034341 response to interferon-gamma
13% GO:0045595 regulation of cell differentiation
13% GO:0045685 regulation of glial cell differentiation
13% GO:0045686 negative regulation of glial cell differentiation
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13% GO:0048514 blood vessel nnorphogenesis
13% GO:0048667 cell nnorphogenesis involved in neuron
differentiation
13% GO:0048713 regulation of oligodendrocyte differentiation
13% GO:0048858 cell projection nnorphogenesis
13% GO:0048869 cellular developmental process
13% GO:0051960 regulation of nervous system development
13% GO:0071229 cellular response to acid
13% GO:0071346 cellular response to interferon-gamma
10% GO:0000079 regulation of cyclin-dependent protein kinase
activity
10% GO:0000089 mitotic metaphase
10% GO:0000902 cell nnorphogenesis
10% GO:0006415 translational termination
10% GO:0010389 regulation of G2/M transition of mitotic cell cycle
10% GO:0016043 cellular component organization
10% GO:0019080 viral genonne expression
10% GO:0019083 viral transcription
10% GO:0021782 glial cell development
10% GO:0030030 cell projection organization
10% GO:0031175 neuron projection development
10% GO:0031397 negative regulation of protein ubiquitination
10% GO:0032989 cellular component nnorphogenesis
10% GO:0032990 cell part nnorphogenesis
10% GO:0034508 centronnere complex assembly
10% GO:0035295 tube development
10% GO:0043200 response to amino acid stimulus
10% GO:0048706 embryonic skeletal system development
10% GO:0048710 regulation of astrocyte differentiation
10% GO:0051323 metaphase
10% GO:0051436 negative regulation of ubiquitin-protein ligase
activity involved in mitotic
cell cycle
10% GO:0060337 type I interferon-mediated signaling pathway
10% GO:0071230 cellular response to amino acid stimulus
10% GO:0071276 cellular response to cadmium ion
10% GO:0071277 cellular response to calcium ion
10% GO:0071357 cellular response to type I interferon
10% GO:0071840 cellular component organization or biogenesis
10% GO:0090068 positive regulation of cell cycle process
6% GO:0000083 regulation of transcription involved in G1/S phase of
mitotic cell cycle
6% GO:0000085 G2 phase of mitotic cell cycle
6% GO:0000910 cytokinesis
6% GO:0001656 nnetanephros development
6% GO:0001838 embryonic epithelial tube formation
6% GO:0002495 antigen processing and presentation of peptide
antigen via MHC class ll
6% GO:0006302 double-strand break repair
6% GO:0006364 rRNA processing
6% GO:0006412 translation
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6% GO:0006414 translational elongation
6% GO:0006928 cellular component movement
6% GO:0006952 defense response
6% GO:0006958 complement activation, classical pathway
6% GO:0007091 mitotic metaphase/anaphase transition
6% GO:0007568 aging
6% GO:0008608 attachment of spindle nnicrotubules to kinetochore
6% GO:0009263 deoxyribonucleotide biosynthetic process
6% GO:0009888 tissue development
6% GO:0010639 negative regulation of organelle organization
6% GO:0010720 positive regulation of cell development
6% GO:0010721 negative regulation of cell development
6% GO:0010812 negative regulation of cell-substrate adhesion
6% GO:0014003 oligodendrocyte development
6% GO:0014015 positive regulation of gliogenesis
6% GO:0016072 rRNA metabolic process
6% GO:0016331 nnorphogenesis of embryonic epithelium
6% GO:0019886 antigen processing and presentation of exogenous
peptide antigen via
MHC class ll
6% GO:0021778 oligodendrocyte cell fate specification
6% GO:0021780 glial cell fate specification
6% GO:0021953 central nervous system neuron differentiation
6% GO:0022613 ribonucleoprotein complex biogenesis
6% GO:0030111 regulation of Wnt receptor signaling pathway
6% GO:0031102 neuron projection regeneration
6% GO:0031400 negative regulation of protein modification process
6% GO:0031960 response to corticosteroid stimulus
6% GO:0032467 positive regulation of cytokinesis
6% GO:0032502 developmental process
6% GO:0032886 regulation of nnicrotubule-based process
6% GO:0032964 collagen biosynthetic process
6% GO:0033043 regulation of organelle organization
6% GO:0033205 cell cycle cytokinesis
6% GO:0034097 response to cytokine stimulus
6% GO:0034621 cellular nnacronnolecular complex subunit organization
6% GO:0034622 cellular nnacronnolecular complex assembly
6% GO:0035019 somatic stem cell maintenance
6% GO:0035148 tube formation
6% GO:0042127 regulation of cell proliferation
6% GO:0042254 ribosome biogenesis
6% GO:0043624 cellular protein complex disassembly
6% GO:0043933 nnacronnolecular complex subunit organization
6% GO:0044259 nnulticellular organisnnal macromolecule metabolic
process
6% GO:0045596 negative regulation of cell differentiation
6% GO:0045786 negative regulation of cell cycle
6% GO:0048736 appendage development
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6% GO:0048741 skeletal muscle fiber development
6% GO:0048747 muscle fiber development
6% GO:0050000 chromosome localization
6% GO:0050769 positive regulation of neurogenesis
6% GO:0051094 positive regulation of developmental process
6% GO:0051128 regulation of cellular component organization
6% GO:0051129 negative regulation of cellular component
organization
6% GO:0051290 protein heterotetrannerization
6% GO:0051303 establishment of chromosome localization
6% GO:0051319 G2 phase
6% GO:0051340 regulation of ligase activity
6% GO:0051352 negative regulation of ligase activity
6% GO:0051437 positive regulation of ubiquitin-protein ligase
activity involved in mitotic
................... cell cycle
6% GO:0051438 regulation of ubiquitin-protein ligase activity
6% GO:0051439 regulation of ubiquitin-protein ligase activity
involved in mitotic cell cycle
6% GO:0051444 negative regulation of ubiquitin-protein ligase
activity
6% GO:0051984 positive regulation of chromosome segregation
6% GO:0055002 striated muscle cell development
6% GO:0055093 response to hyperoxia
6% GO:0060173 limb development
6% GO:0060333 interferon-gamma-mediated signaling pathway
6% GO:0060541 respiratory system development
6% GO:0060564 negative regulation of mitotic anaphase-promoting
complex activity
6% GO:0070208 protein heterotrinnerization
6% GO:0070507 regulation of nnicrotubule cytoskeleton organization
6% GO:0070777 D-aspartate transport
6% GO:0070779 D-aspartate import
6% GO:0071248 cellular response to metal ion
6% GO:0071775 regulation of cell cycle cytokinesis
6% GO:0071777 positive regulation of cell cycle cytokinesis
6% GO:0072001 renal system development
6% GO:0072006 nephron development
6% GO:0072175 epithelial tube formation
6% GO:0090090 negative regulation of canonical Wnt receptor
signaling pathway
6% GO:2000736 regulation of stem cell differentiation
3% GO:0000077 DNA damage checkpoint
3% GO:0000086 G2/M transition of mitotic cell cycle
3% GO:0000184 nuclear-transcribed nnRNA catabolic process, nonsense-
mediated decay
3% GO:0000956 nuclear-transcribed nnRNA catabolic process
3% GO:0001503 ossification
3% GO:0001655 urogenital system development
3% GO:0001666 response to hypoxia
3% GO:0001763 nnorphogenesis of a branching structure
3% GO:0001822 kidney development
3% GO:0001841 neural tube formation
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3% GO:0001843 neural tube closure
3% GO:0002455 hunnoral immune response mediated by circulating
innnnunoglobulin
3% GO:0002480 antigen processing and presentation of exogenous
peptide antigen via
................... MHC class I, TAP-independent
3% GO:0002544 chronic inflammatory response
3% GO:0002576 platelet degranulation
3% GO:0002685 regulation of leukocyte migration
3% GO:0002687 positive regulation of leukocyte migration
3% GO:0002688 regulation of leukocyte chennotaxis
3% GO:0002690 positive regulation of leukocyte chennotaxis
3% GO:0003002 regionalization
3% GO:0003105 negative regulation of glonnerular filtration
3% GO:0003170 heart valve development
3% GO:0003179 heart valve nnorphogenesis
3% GO:0003207 cardiac chamber formation
3% GO:0003211 cardiac ventricle formation
3% GO:0003281 ventricular septum development
3% GO:0006119 oxidative phosphorylation
3% GO:0006120 nnitochondrial electron transport, NADH to ubiquinone
3% GO:0006139 nucleobase-containing compound metabolic process
3% GO:0006221 pyrinnidine nucleotide biosynthetic process
3% GO:0006325 chromatin organization
3% GO:0006396 RNA processing
3% GO:0006401 RNA catabolic process
3% GO:0006402 nnRNA catabolic process
3% GO:0006413 translational initiation
3% GO:0006563 L-serine metabolic process
3% GO:0006564 L-serine biosynthetic process
3% GO:0006612 protein targeting to membrane
3% GO:0006613 cotranslational protein targeting to membrane
3% GO:0006614 SRP-dependent cotranslational protein targeting to
membrane
3% GO:0006807 nitrogen compound metabolic process
3% GO:0006935 chennotaxis
3% GO:0006950 response to stress
3% GO:0006955 immune response
3% GO:0006956 complement activation
3% GO:0007010 cytoskeleton organization
3% GO:0007062 sister chromatid cohesion
3% GO:0007126 meiosis
3% GO:0007127 meiosis I
3% GO:0007162 negative regulation of cell adhesion
3% GO:0007219 Notch signaling pathway
3% GO:0007263 nitric oxide mediated signal transduction
3% GO:0007272 ensheathnnent of neurons
3% GO:0007389 pattern specification process
3% GO:0007411 axon guidance
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3% GO:0007420 brain development
3% GO:0008283 cell proliferation
3% GO:0008285 negative regulation of cell proliferation
3% GO:0008344 adult loconnotory behavior
3% GO:0008347 glial cell migration
3% GO:0008366 axon ensheathnnent
3% GO:0009059 macromolecule biosynthetic process
3% GO:0009147 pyrinnidine nucleoside triphosphate metabolic process
3% GO:0009148 pyrinnidine nucleoside triphosphate biosynthetic
process
3% GO:0009186 deoxyribonucleoside diphosphate metabolic process
3% GO:0009262 deoxyribonucleotide metabolic process
3% GO:0009605 response to external stimulus
3% GO:0009607 response to biotic stimulus
3% GO:0009611 response to wounding
3% GO:0009612 response to mechanical stimulus
3% GO:0009615 response to virus
3% GO:0009628 response to abiotic stimulus
3% GO:0009954 proximal/distal pattern formation
3% GO:0010033 response to organic substance
3% GO:0010243 response to organic nitrogen
3% GO:0010467 gene expression
3% GO:0010498 proteasonnal protein catabolic process
3% GO:0010594 regulation of endothelial cell migration
3% GO:0010718 positive regulation of epithelial to nnesenchynnal
transition
3% GO:0010759 positive regulation of macrophage chennotaxis
3% GO:0010769 regulation of cell nnorphogenesis involved in
differentiation
3% GO:0010770 positive regulation of cell nnorphogenesis involved
in differentiation
3% GO:0010975 regulation of neuron projection development
3% GO:0010977 negative regulation of neuron projection development
3% GO:0014020 primary neural tube formation
3% GO:0014052 regulation of gamma-anninobutyric acid secretion
3% GO:0014054 positive regulation of gamma-anninobutyric acid
secretion
3% GO:0014070 response to organic cyclic compound
3% GO:0014075 response to amine stimulus
3% GO:0014706 striated muscle tissue development
3% GO:0014812 muscle cell migration
3% GO:0015949 nucleobase-containing small molecule interconversion
3% GO:0015980 energy derivation by oxidation of organic compounds
3% GO:0016064 innnnunoglobulin mediated immune response
3% GO:0016070 RNA metabolic process
3% GO:0016071 nnRNA metabolic process
3% GO:0016477 cell migration
3% GO:0016525 negative regulation of angiogenesis
3% GO:0018149 peptide cross-linking
3% GO:0019058 viral infectious cycle
3% GO:0019221 cytokine-mediated signaling pathway
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3% GO:0019228 regulation of action potential in neuron
3% GO:0019724 B cell mediated immunity
3% GO:0019827 stem cell maintenance
3% GO:0019985 translesion synthesis
3% GO:0021510 spinal cord development
3% GO:0021517 ventral spinal cord development
3% GO:0021522 spinal cord motor neuron differentiation
3% GO:0021542 dentate gyrus development
3% GO:0021779 oligodendrocyte cell fate commitment
3% GO:0021915 neural tube development
3% GO:0022411 cellular component disassembly
3% GO:0022415 viral reproductive process
3% GO:0022604 regulation of cell nnorphogenesis
3% GO:0022900 electron transport chain
3% GO:0022904 respiratory electron transport chain
3% GO:0030178 negative regulation of Wnt receptor signaling pathway
3% GO:0030204 chondroitin sulfate metabolic process
3% GO:0030278 regulation of ossification
3% GO:0030324 lung development
3% GO:0030334 regulation of cell migration
3% GO:0030513 positive regulation of BMP signaling pathway
3% GO:0030514 negative regulation of BMP signaling pathway
3% GO:0031060 regulation of histone nnethylation
3% GO:0031103 axon regeneration
3% GO:0031109 nnicrotubule polymerization or depolynnerization
3% GO:0031115 negative regulation of nnicrotubule polymerization
3% GO:0031338 regulation of vesicle fusion
3% GO:0031340 positive regulation of vesicle fusion
3% GO:0031570 DNA integrity checkpoint
3% GO:0032331 negative regulation of chondrocyte differentiation
3% GO:0032355 response to estradiol stimulus
3% GO:0032387 negative regulation of intracellular transport
3% GO:0032963 collagen metabolic process
3% GO:0032984 nnacronnolecular complex disassembly
3% GO:0034470 ncRNA processing
3% GO:0034599 cellular response to oxidative stress
3% GO:0034614 cellular response to reactive oxygen species
3% GO:0034623 cellular nnacronnolecular complex disassembly
3% GO:0034641 cellular nitrogen compound metabolic process
3% GO:0034644 cellular response to UV
3% GO:0034645 cellular macromolecule biosynthetic process
3% GO:0034660 ncRNA metabolic process
3% GO:0035107 appendage nnorphogenesis
3% GO:0035108 limb nnorphogenesis
3% GO:0035457 cellular response to interferon-alpha
3% GO:0035909 aorta nnorphogenesis
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3% GO:0035988 chondrocyte proliferation
3% GO:0040001 establishment of mitotic spindle localization
3% GO:0040011 locomotion
3% GO:0040012 regulation of locomotion
3% GO:0040034 regulation of development, heterochronic
3% GO:0042060 wound healing
3% GO:0042273 ribosomal large subunit biogenesis
3% GO:0042330 taxis
3% GO:0042476 odontogenesis
3% GO:0042493 response to drug
3% GO:0042552 nnyelination
3% GO:0042692 muscle cell differentiation
3% GO:0042773 ATP synthesis coupled electron transport
3% GO:0042775 mitochondria! ATP synthesis coupled electron
transport
3% GO:0043161 proteasonnal ubiquitin-dependent protein catabolic
process
3% GO:0043241 protein complex disassembly
3% GO:0043407 negative regulation of MAP kinase activity
3% GO:0044236 nnulticellular organisnnal metabolic process
3% GO:0045047 protein targeting to ER
3% GO:0045087 innate immune response
3% GO:0045333 cellular respiration
3% GO:0045597 positive regulation of cell differentiation
3% GO:0045667 regulation of osteoblast differentiation
3% GO:0045746 negative regulation of Notch signaling pathway
3% GO:0045765 regulation of angiogenesis
3% GO:0045766 positive regulation of angiogenesis
3% GO:0045768 positive regulation of anti-apoptosis
3% GO:0045837 negative regulation of membrane potential
3% GO:0045840 positive regulation of mitosis
3% GO:0046622 positive regulation of organ growth
3% GO:0048008 platelet-derived growth factor receptor signaling
pathway
3% GO:0048145 regulation of fibroblast proliferation
3% GO:0048505 regulation of timing of cell differentiation
3% GO:0048545 response to steroid hormone stimulus
3% GO:0048562 embryonic organ nnorphogenesis
3% GO:0048568 embryonic organ development
3% GO:0048598 embryonic nnorphogenesis
3% GO:0048641 regulation of skeletal muscle tissue development
3% GO:0048678 response to axon injury
3% GO:0048704 embryonic skeletal system nnorphogenesis
3% GO:0048708 astrocyte differentiation
3% GO:0048714 positive regulation of oligodendrocyte
differentiation
3% GO:0048715 negative regulation of oligodendrocyte
differentiation
3% GO:0048742 regulation of skeletal muscle fiber development
3% GO:0048771 tissue remodeling
3% GO:0048863 stem cell differentiation
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3% GO:0048864 stem cell development
3% GO:0048870 cell motility
3% GO:0050654 chondroitin sulfate proteoglycan metabolic process
3% GO:0050657 nucleic acid transport
3% GO:0050658 RNA transport
3% GO:0050678 regulation of epithelial cell proliferation
3% GO:0050679 positive regulation of epithelial cell proliferation
3% GO:0050768 negative regulation of neurogenesis
3% GO:0050773 regulation of dendrite development
3% GO:0050808 synapse organization
3% GO:0050920 regulation of chennotaxis
3% GO:0051028 nnRNA transport
3% GO:0051095 regulation of helicase activity
3% GO:0051099 positive regulation of binding
3% GO:0051100 negative regulation of binding
3% GO:0051146 striated muscle cell differentiation
3% GO:0051153 regulation of striated muscle cell differentiation
3% GO:0051216 cartilage development
3% GO:0051225 spindle assembly
3% GO:0051236 establishment of RNA localization
3% GO:0051239 regulation of nnulticellular organisnnal process
3% GO:0051256 spindle nnidzone assembly involved in mitosis
3% GO:0051270 regulation of cellular component movement
3% GO:0051293 establishment of spindle localization
3% GO:0051305 chromosome movement towards spindle pole
3% GO:0051321 meiotic cell cycle
3% GO:0051327 M phase of meiotic cell cycle
3% GO:0051382 kinetochore assembly
3% GO:0051384 response to glucocorticoid stimulus
3% GO:0051443 positive regulation of ubiquitin-protein ligase
activity
3% GO:0051569 regulation of histone H3-K4 nnethylation
3% GO:0051571 positive regulation of histone H3-K4 nnethylation
3% GO:0051592 response to calcium ion
3% GO:0051653 spindle localization
3% GO:0051656 establishment of organelle localization
3% GO:0051674 localization of cell
3% GO:0051707 response to other organism
3% GO:0051785 positive regulation of nuclear division
3% GO:0051823 regulation of synapse structural plasticity
3% GO:0051957 positive regulation of amino acid transport
3% GO:0055001 muscle cell development
3% GO:0060056 mammary gland involution
3% GO:0060071 Wnt receptor signaling pathway, planar cell polarity
pathway
3% GO:0060174 limb bud formation
3% GO:0060219 camera-type eye photoreceptor cell differentiation
3% GO:0060249 anatomical structure homeostasis
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3% GO:0060429 epithelium development
3% GO:0060537 muscle tissue development
3% GO:0060606 tube closure
3% GO:0060828 regulation of canonical Wnt receptor signaling pathway
3% GO:0060900 embryonic camera-type eye formation
3% GO:0060993 kidney nnorphogenesis
3% GO:0060998 regulation of dendritic spine development
3% GO:0061001 regulation of dendritic spine nnorphogenesis
3% GO:0061326 renal tubule development
3% GO:0061333 renal tubule nnorphogenesis
3% GO:0065003 nnacronnolecular complex assembly
3% GO:0070206 protein trinnerization
3% GO:0070482 response to oxygen levels
3% GO:0070972 protein localization in endoplasnnic reticulunn
3% GO:0071294 cellular response to zinc ion
3% GO:0071310 cellular response to organic substance
3% GO:0071345 cellular response to cytokine stimulus
3% GO:0071417 cellular response to organic nitrogen
3% GO:0071418 cellular response to amine stimulus
3% GO:0071453 cellular response to oxygen levels
3% GO:0071504 cellular response to heparin
3% GO:0071822 protein complex subunit organization
3% GO:0071843 cellular component biogenesis at cellular level
3% GO:0071845 cellular component disassembly at cellular level
3% GO:0071901 negative regulation of protein serine/threonine
kinase activity
3% GO:0072009 nephron epithelium development
3% GO:0072028 nephron nnorphogenesis
3% GO:0072073 kidney epithelium development
3% GO:0072078 nephron tubule nnorphogenesis
3% GO:0072079 nephron tubule formation
3% GO:0072080 nephron tubule development
3% GO:0072088 nephron epithelium nnorphogenesis
3% GO:0072170 nnetanephric tubule development
3% GO:0072207 nnetanephric epithelium development
3% GO:0072210 nnetanephric nephron development
3% GO:0072224 nnetanephric glonnerulus development
3% GO:0072234 nnetanephric nephron tubule development
3% GO:0072243 nnetanephric nephron epithelium development
3% GO:0072594 establishment of protein localization to organelle
3% GO:0072599 establishment of protein localization in endoplasnnic
reticulunn
3% GO:0090092 regulation of transnnennbrane receptor protein
serine/threonine kinase
signaling pathway
3% GO:0090101 negative regulation of transnnennbrane receptor
protein serine/threonine
kinase signaling pathway
3% GO:0090175 regulation of establishment of planar polarity
3% GO:0090304 nucleic acid metabolic process
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3% GO:0097066 response to thyroid hormone stimulus
3% GO:0097067 cellular response to thyroid hormone stimulus
3% GO:2000097 regulation of smooth muscle cell-matrix adhesion
3% GO:2000145 regulation of cell motility
3% GO:2000177 regulation of neural precursor cell proliferation
3% GO:2000179 positive regulation of neural precursor cell
proliferation
3% GO:2000602 regulation of interphase of mitotic cell cycle
The % of individual tumors within a subgroup that are enriched for a specific
GO term is
shown, ordered by decreasing representation. Neurodevelopmental terms are
highlighted with
bolded text.
Discussion
The major finding is that AKT pathway genes classify GBM into at least five
patient
subgroups with unique clinical and molecular characteristics. The results were
validated in an
independent dataset of non-overlapping samples, suggesting AKT classes reflect
underlying
structure in the data and do not arise from chance or technical artifacts such
as batch effects and
patient sampling. Taken together these data add to previous results suggesting
histopathologically diagnosed GBM is a collection of molecular subgroups with
fundamental
differences in biology and clinical behavior. This approach advances
classification of GBM by
splitting out groups not previously identified by other approaches and expands
the understanding
of molecular aberrations underlying subgroups.
The inventors interpret with caution the finding that SL patients treated with
BCNU or
CCNU have appreciably longer survival than SL patients receiving other
treatments (median
survival 5.8 vs. 1.05 years respectively). Inhomogeneity between the cohorts
(including
treatment protocols and institution providing tumor) could impact survival.
However, age and
IDH1 mutation status clearly do not contribute since patients in the longer
surviving cohort were
older and had less IDH1 mutations. These results suggest AKT classification is
a predictive
marker that identifies a subset of GBM patients with sensitivity to BCNU/CCNU.
Interestingly,
there is a subset of anaplastic oligodendroglial tumors characterized by 1p19q
loss of
heterozygosity (LOH) and IDH1 mutations that significantly benefits from
procarbazine, CCNU,
and vincristine (PCV) chemotherapy [35]. This anaplastic oligodendroglial
subtype shares
similarities to the AKT SL subgroup (19q loss and IDH1 mutant tumors).
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Mutations in IDH1 are a common and early event in low grade glioma, they are
present
in secondary GBM [36], [37], [38] and may cause the G-CIMP phenotype [36],
[37], [38], [39].
One third of SL tumors have IDH1 mutations and CIMP. This subgroup also has
other molecular
similarities to secondary tumors (enriched for genomic alterations in TP53 and
PDGFRA),
longer survival and a tendency for less endothelial proliferation and
pallisading necrosis (Figures
12 and 13). These data suggest tumors in the SL subtype are grade IV secondary
tumors or
borderline grade III/IV secondary tumors progressing to GBM. If this is true
then genomic
alterations associated with the SL subtype might be used as markers of
progression for grade
II/III secondary tumors. These results also indicate there is a population of
GBM without IDH1
mutations that share clinical characteristics and a similar pattern of AKT
pathway gene
expression with the IDH1 mutant tumors. This suggests other paths beside IDH1
mutation give
rise to the IDH1 mutant/CIMP phenotype.
The inventors found distinct patterns of expression for PI3K/AKT/mTOR
components in
subgroups. The inventors' results suggest gene products that inhibit AKT and
mTOR are
important regulators of PI3K/AKT/mTOR/S6 axis output. In the inventors' model
the loss of
AKT and mTOR inhibitors (PHLPP, TSC and pAMPK) increases output of the
AKT/mTOR/S6
axis in the MES subgroup. Conversely, increased expression of these inhibitors
decreases output
in the SL subgroup. In an apparent paradox, p-AKT expression is low in the MES
subgroup.
While not wishing to be bound by any theory, the inventors suggest AKT
phosphorylation is held
in check in the MES subgroup by (1) heightened activity of an mTOR/S6K/IRS1
negative
feedback loop [40], [41], [42], [43] and (2) low TSC1 and 2 expression that
decreases mTORC2
activation and AKT phosphorylation [42], [44]. The inventors' model suggests
the MES subtype
will be sensitive to joint inhibition of mTOR and PI3K, but inhibition of mTOR
alone will
increase p-AKT. Interestingly, NF1 loss drives mTOR/S6 hyper-activation via
AKT [45], [46],
[47] and the MES subtype is enriched for NF1 loss. These data suggest
subgroups have
variations in AKT pathway signaling that will affect sensitivity to pathway
inhibitors.
How do these results compare with other approaches that use mRNA to classify
GBM?
AKT classification is complementary to previous classification methods but
divides GBM into
more subgroups. It gives patient subgroups with statistically significant
differences in survival
while Phillips [4] or TCGA [10] methods do not when using the same database.
Interestingly,
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there was higher concordance between AKT classification and classification
based on survival-
associated mRNA used by Phillips et. al. [4] than most variable mRNA used by
Verhaak et.
al.[10]. Without wishing to be bound by any particular theory, the inventors
believe classification
schemes based on mRNA relevant to tumorigenicity, like survival-associated and
AKT pathway
genes, are more effective at partitioning tumors into clinically and
molecularly relevant groups.
Survival differences found in the discovery dataset were diminished in the
validation
dataset. Inhomogeneity's between datasets that could confound comparisons
including (1) age
(median age = 49 yrs. in discovery vs. 59 yrs. in validation dataset), (2)
patient populations (three
institutions contributed tumors to the discovery and eighteen to the
validation dataset), (3)
treatment (there were large variations in treatment regimens in the validation
dataset).
One AKT subgroup was not found in the validation dataset (C1). While not
wishing to be
bound by any theory, morphological heterogeneity can result in inconsistent
intra- and inter-
observer diagnosis of grade and histological type (astrocytoma,
oligodendroglioma and mixed
oligoastrocytoma) [48], [49], [50]. Therefore Cl may be a histological variant
diagnosed as
GBM and included in the discovery, but not the validation dataset.
GO term analysis suggests different cells of origin/dominant biological
processes for
each subgroup (summarized in Figure 8A and B). The younger, longer surviving,
SL patient
subgroup with molecular similarities to secondary GBM had terms associated
with both neuro-
and glio-genesis suggesting a NSC cell of origin. Indeed, the longer survival
of these patients is
consistent with the quiescent nature of NSC. PROLIF tumors also contained
neuro- and glio-
genesis terms in addition to terms related to mitosis, spindle formation and
cell cycle checkpoint.
Literature suggests the balance between symmetric and asymmetric cell
divisions regulates NSC
[51] which is influenced by proteins with a role in spindle formation and
mitotic progression
[52]. Based on this and their aggressive nature, while not wishing to be bound
by any theory, the
inventors believe that PROLIF tumors are derived from NSC with enforced
symmetric cell
divisions that rapidly expand the population (Figure 8B). The ability of AKT
classification to
group tumors by cell of origin would suggest a major role for the PI3K/AKT
pathway in
neurodevelopment. This is consistent with reports showing a role for pathway
members in NSC
maintenance [53], [54].
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The inventors show that AKT-based classification can augment drug development
on
many levels. This work indicates evaluating new drugs using all GBM patients
combined with
different natural courses and/or response to therapy can confound clinical
trials. It suggests
incorporating AKT classification can improve clinical trial design, decreasing
their cost and
maximizing the number of therapeutics that can be evaluated. In addition, AKT
based
classification can enhance drug discovery since new pathways and drug targets
will be easier to
find in molecularly homogeneous samples. The inventors demonstrate that robust
molecular
classification of GBM can ultimately improve patient care by guiding
therapeutic planning,
sparing patients ineffective treatments, both standard and experimental, and
focusing on
strategies more likely to work.
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The various methods and techniques described above provide a number of ways to
carry
out the application. Of course, it is to be understood that not necessarily
all objectives or
advantages described can be achieved in accordance with any particular
embodiment described
herein. Thus, for example, those skilled in the art will recognize that the
methods can be
performed in a manner that achieves or optimizes one advantage or group of
advantages as
taught herein without necessarily achieving other objectives or advantages as
taught or suggested
herein. A variety of alternatives are mentioned herein. It is to be understood
that some preferred
embodiments specifically include one, another, or several features, while
others specifically
exclude one, another, or several features, while still others mitigate a
particular feature by
inclusion of one, another, or several advantageous features.
Furthermore, the skilled artisan will recognize the applicability of various
features from
different embodiments. Similarly, the various elements, features and steps
discussed above, as
well as other known equivalents for each such element, feature or step, can be
employed in
various combinations by one of ordinary skill in this art to perform methods
in accordance with
the principles described herein. Among the various elements, features, and
steps some will be
specifically included and others specifically excluded in diverse embodiments.
Although the application has been disclosed in the context of certain
embodiments and
examples, it will be understood by those skilled in the art that the
embodiments of the application
extend beyond the specifically disclosed embodiments to other alternative
embodiments and/or
uses and modifications and equivalents thereof.
Preferred embodiments of this application are described herein, including the
best mode
known to the inventors for carrying out the application. Variations on those
preferred
embodiments will become apparent to those of ordinary skill in the art upon
reading the
foregoing description. It is contemplated that skilled artisans can employ
such variations as
appropriate, and the application can be practiced otherwise than specifically
described herein.
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Accordingly, many embodiments of this application include all modifications
and equivalents of
the subject matter recited in the claims appended hereto as permitted by
applicable law.
Moreover, any combination of the above-described elements in all possible
variations thereof is
encompassed by the application unless otherwise indicated herein or otherwise
clearly
contradicted by context.
All patents, patent applications, publications of patent applications, and
other material,
such as articles, books, specifications, publications, documents, things,
and/or the like,
referenced herein are hereby incorporated herein by this reference in their
entirety for all
purposes, excepting any prosecution file history associated with same, any of
same that is
inconsistent with or in conflict with the present document, or any of same
that may have a
limiting affect as to the broadest scope of the claims now or later associated
with the present
document. By way of example, should there be any inconsistency or conflict
between the
description, definition, and/or the use of a term associated with any of the
incorporated material
and that associated with the present document, the description, definition,
and/or the use of the
term in the present document shall prevail.
It is to be understood that the embodiments of the application disclosed
herein are
illustrative of the principles of the embodiments of the application. Other
modifications that can
be employed can be within the scope of the application. Thus, by way of
example, but not of
limitation, alternative configurations of the embodiments of the application
can be utilized in
accordance with the teachings herein. Accordingly, embodiments of the present
application are
not limited to that precisely as shown and described.
Various embodiments of the invention are described above in the Detailed
Description.
While these descriptions directly describe the above embodiments, it is
understood that those
skilled in the art may conceive modifications and/or variations to the
specific embodiments
shown and described herein. Any such modifications or variations that fall
within the purview of
this description are intended to be included therein as well. Unless
specifically noted, it is the
intention of the inventors that the words and phrases in the specification and
claims be given the
ordinary and accustomed meanings to those of ordinary skill in the applicable
art(s).
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The foregoing description of various embodiments of the invention known to the
applicant at this time of filing the application has been presented and is
intended for the purposes
of illustration and description. The present description is not intended to be
exhaustive nor limit
the invention to the precise form disclosed and many modifications and
variations are possible in
the light of the above teachings. The embodiments described serve to explain
the principles of
the invention and its practical application and to enable others skilled in
the art to utilize the
invention in various embodiments and with various modifications as are suited
to the particular
use contemplated. Therefore, it is intended that the invention not be limited
to the particular
embodiments disclosed for carrying out the invention.
While particular embodiments of the present invention have been shown and
described, it
will be obvious to those skilled in the art that, based upon the teachings
herein, changes and
modifications may be made without departing from this invention and its
broader aspects and,
therefore, the appended claims are to encompass within their scope all such
changes and
modifications as are within the true spirit and scope of this invention.
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