U.S. patent application number 10/083550 was filed with the patent office on 2003-03-27 for method for evaluating dna probes position on substrate.
Invention is credited to Rokutan, Kazuhito, Saito, Toshiro, Tomita, Hiroyuki.
Application Number | 20030059791 10/083550 |
Document ID | / |
Family ID | 26610254 |
Filed Date | 2003-03-27 |
United States Patent
Application |
20030059791 |
Kind Code |
A1 |
Rokutan, Kazuhito ; et
al. |
March 27, 2003 |
Method for evaluating DNA probes position on substrate
Abstract
An oligonucleotide array comprising an array of multiple
oligonucleotides with different base sequences fixed onto known and
separate positions on a support substrate, wherein said
oligonucleotides are biological stress related genes or
complementary sequence chains to the said genes, and the said
oligonucleotides are classified according to their gene functions,
wherein the fixation region on the support substrate is divided
into the said classification.
Inventors: |
Rokutan, Kazuhito; (Osaka,
JP) ; Tomita, Hiroyuki; (Tachikawa, JP) ;
Saito, Toshiro; (Hatoyama, JP) |
Correspondence
Address: |
REED SMITH LLP
Suite 1400
3110 Fairview Drive
Falls Church
VA
22042
US
|
Family ID: |
26610254 |
Appl. No.: |
10/083550 |
Filed: |
February 27, 2002 |
Current U.S.
Class: |
435/6.1 ;
435/287.2; 702/20 |
Current CPC
Class: |
C12Q 2600/158 20130101;
G16B 25/20 20190201; G16B 25/00 20190201; C12Q 2600/166 20130101;
C12Q 2565/513 20130101; G16B 25/30 20190201; C12Q 1/6883
20130101 |
Class at
Publication: |
435/6 ;
435/287.2; 702/20 |
International
Class: |
C12Q 001/68; G06F
019/00; G01N 033/48; G01N 033/50; C12M 001/34 |
Foreign Application Data
Date |
Code |
Application Number |
Feb 28, 2001 |
JP |
2001-053465 |
Jan 31, 2002 |
JP |
2002-022682 |
Claims
What is claimed is:
1. An oligonucleotide array comprising an array of multiple
oligonucleotides with different base sequences fixed onto known and
separate positions on a support substrate, wherein said
oligonucleotides are biological stress related genes or
complementary sequence chains to the said genes, and the said
oligonucleotides are classified according to their gene functions,
wherein the fixation region on the support substrate is divided
into the said classification.
2. An oligonucleotide array comprising multiple subblock regions
and oligonucleotides with different base sequences positioned to
each of said multiple subblock regions, wherein said
oligonucleotides are positioned according to an arrangement pattern
wherein oligonucleotides with a first correlation degree are
positioned closer to each other than oligonucleotides that have a
lower correlation degree.
3. The oligonucleotide array according to claim 2 wherein said
oligonucleotides are oligonucleotides related to a particular
phenotype.
4. The oligonucleotide array according to claim 2 wherein said
phenotype is related to stress response.
5. The oligonucleotide array according to claim 4 wherein said
oligonucleotides are one of the following: internal or external
standard genes for calibration, stress tolerance or survival
related genes and hormonal genes, cytokine genes, apoptosis
inducing genes, glucocorticoid and other anti-inflammation related
genes and growth repressor genes, immune response related
transcription factors and signaling molecules, cell disorder
triggering cytokine inductive transcription factors and signaling
molecules, growth inhibition related transcription factors and
signaling molecules, stress tolerance related transcription factors
and signaling molecules.
6. The oligonucleotide array according to claim 2 wherein said
correlation degrees are those determined in a database.
7. The oligonucleotide array according to claim 6 wherein said
correlation degrees are determined by one or a combination of two
or more of gene inter-relationship score, pairwise information of
ligand and receptor, protein-protein interaction information, and
gene passway information.
8. The oligonucleotide array according to claim 2 wherein said
correlation degree is statistically calculated from expression
amount of experimental results using samples for comparison,
wherein classification algorithm used comprises either one of P
value, FDD, SVM and others.
9. The oligonucleotide array according to claim 8 wherein said
samples comprise samples from patients with a particular disease
and samples from healthy subjects.
10. A method of evaluating label detection of hybridization wherein
labeled cell-derived RNA are hybridized to an oligonucleotide array
comprising multiple subblock regions and oligonucleotides with
different base sequences positioned to each of said multiple
subblock regions, wherein said oligonucleotides are positioned
according to an arrangement pattern wherein oligonucleotides with a
first correlation degree are positioned closer to each other than
oligonucleotides that have a lower correlation degree; and said
hybridization is label detected.
Description
BACKGROUND OF THE INVENTION
[0001] (1) Field of the Invention
[0002] This Invention concerns a DNA array and an analytical method
of stress using said DNA array for the simple evaluation of degrees
of stress. This Invention also concerns a method of evaluation of
expression of gene groups related to certain diseases, not limiting
to stress, by positioning oligonucleotides on substrate based on
degree of correlation.
[0003] (2) Description of the Related Art
[0004] Increases in diseases associated with life style and atopic
allergy are one of the factors that are responsible for the
increase in today's medical burden to the nation. Reported also are
increases in the numbers of suicides, lowering age of criminals and
increases in patients with post-traumatic stress disorder (PTSD).
Medical experts agree that stress play a role in background or life
style-associated diseases, allergy, suicide, crime and PTSD.
[0005] Stress is defined as a reaction of the living body to sudden
invasion, both as specific reaction to each invasion and as generic
non-specific reaction, which has a fixed pattern regardless of the
type of invasion. Stress-causing stimuli, or stressor, include
abnormal temperature, burn, inflammation, immune reaction, noise,
electric shock, ultraviolet light, bacterial toxin, bacteria,
virus, operation, exercise, pain stimulus, physical restrain,
hypoxia, hypoglycemia, ischemia, tests, interpersonal friction,
deaths of relatives, loneliness, broken heart, despair,
disappointment, social unrest, war, terrorism and earth quake. With
advancement in knowledge of the maintenance mechanism of bodily
homeostasis, it has become clear that there is a close relationship
between abnormalities of the three major regulatory mechanisms of
the body, the nerve, endocrine and immune system, and stress.
[0006] In conventional oligonucleotide array, it is decided first
which genes are placed on chips, and then, according to the order,
such as alphabetical order, designated to genes, genes are placed
on a plate, such as a 96-well plate, using a spotter with several
needles. In this method, although genes are lined up
systematically, a step is required at the actual evaluation to
confirm the positions of genes by consulting address information on
files and images that show where and which genes are placed.
[0007] However, no medicophysiological diagnostic method has been
developed by which the degree of stress can be evaluated
objectively. For instance, blood concentrations of stress hormones,
such as catecholamine and adrenocortical hormone, vary greatly
among individuals and change with time. In other words, blood
concentrations of stress hormones do not change uniformly in
response to stress stimuli, and are known to be insufficient to be
used for evaluation of degree of stress. In addition, it is
extremely difficult to evaluate bodily reactions only by measuring
these limited stress hormones because stress is the reaction of
complex systems, requiring multilateral evaluations. Stress also is
studied in the field of social psychology. Psychological tests in
the form of interviews or questionnaires have been developed to
evaluate degree of stress. However, it cannot be said that
psychological tests substantiate sufficiently physiological
reaction of the body. That is to say, currently, there scarcely are
methods for objective evaluation of stress of individual persons.
However, stress is an important phenomenon that is related to
abnormalities of the automatic nervous system, endocrine and
immune, gastric ulcer, acute lesions of gastric mucus, mental
diseases and reproductive dysfunction. If it is possible to
evaluate degree of stress readily at not only specialty medical
organizations but also general practitioners, health facilities at
business and school and health screening centers, it is a useful
measure, as feedback can be implemented in daily life at home,
workplace and school. From that standpoint, development of
diagnostic instruments is sought that can determine the degree of
stress.
[0008] The objective of this Invention is to provide a diagnostic
method, specifically, oligonucleotide array, by which degrees of
stress can be determined readily and at low cost. In particular,
this Invention aims at minimizing the number of DNA fragments
placed on the array by specifying groups of genes, which are
imperative in determination of degrees of stress, and at providing
an array for stress analysis with high reproducibility and
reliability. This Invention also aims at instant evaluation of the
correlation between genes that are related a certain disease by
devising regulations in how genes are arranged.
SUMMARY OF THE INVENTION
[0009] As mentioned above, stress is the complex reaction in which
various organs, such as the nervous, endocrine and immune systems,
play roles and must be evaluated from many angles. Expressed at the
gene level, stress reaction, which is a phenomenon with complex
sources, occurs when the on-and-off switches of groups of genes
related to stress are turned on, the volume of stress-related
protein increases or decreases. The body mechanism is thought to be
regulated according to the balance in activities of the whole
protein. In other words, abnormalities of the on-and-off mechanism
in stress-related gene groups induce the abnormalities of the
balance in protein activities, -resulting in the abnormalities of
regulation of body mechanism, or occurrence of stress. The
switching on and off of genes is controlled, for example, by
increases or decreases in the level of gene expression. The level
of gene expression can be measured using the level of messenger RNA
or the level of protein as an index. With techniques currently
available, the measurement can be performed extremely easily using
the level of messenger RNA as an index rather than using the level
of protein. Therefore, stress is evaluated easily by observing the
increase or decrease in the level of expression of messenger RNA of
several stress-related genes. DNA array (also called
oligonucleotide array) developed recently is the most suitable for
this purpose.
[0010] Here, the state of expression is explained in detail. The
state of expression is one of genotype, and expression in the term
"the state of expression" means the state, where the region of
genes on DNA is transcripted on to RNA, or protein is translated
through transcribed RNA. The state in the term "the state of
expression" means a row of "n" pieces of genes, or gene 1, gene 2,
so forth, ending with gene "n". When ON indicates that expression
takes place and OFF indicated that expression does not take place,
there is a row of (ON or OFF), (ON or OFF), repeating "n" times;
this is called "state". When with "n" pieces of genes, UP indicates
increased level of RNA transcription, EVEN indicate unchanged, and
DOWN indicates decreased, there is a row of (UP, EVEN or DOWN),
(UP, EVEN or DOWN), repeating "n" times; this is called "state".
The correlation between 2 genes, any 2 among "n" pieces of genes,
is "state", that is to say, when the intensity of measurement
signal of gene i is X and the intensity of measurement signal of
gene j is Y, and mean of X and Y in N times of experiments are m(X)
and m(Y), and standard deviations are S(X) and S(Y), respectively,
the matrix of the correlation coefficient "r", or r(i,j) is
"state". Correlation coefficient can be expressed, for example, in
the following equation (1). 1 r ( i , j ) = k = 1 N ( X - m ( X ) )
/ S ( X ) .times. ( Y - m ( Y ) ) / S ( Y ) ) / ( N - 1 ) ( 1 )
[0011] Changes in the above-mentioned the state expression, that
is, changes in genotype induce changes in phenotype. Phenotype
means phenomenon that can be observed from outside by some means.
Phenotype, for example is disease or symptoms and sites of the body
where symptoms appear. Disease is a pathophysiological state that
physicians can diagnose by experience, such as diabetes mellitus
and cancer. Symptom is a phenomenon persons feel subjectively, such
as headache and abdominal pain. Symptom also is different from
normal values that can be detected by test apparatus; for example,
neutral fat is above the standard value in obesity. Included also
in phenotype are some things that can be observed from outside by
some means, excluding difference in cell configuration and in
velocity of cell growth.
[0012] DNA array (oligonucleotide array) comprises plural DNA
fragments (oligonucleotide) that are fixed on substrate. Each
nucleotide corresponds to different genes. In measurement,
complementary DNA (cDNA) fragments are synthesized in reaction with
reverse transcriptase using messenger RNA as a template. At the
time of the reaction with reverse transcriptase, an appropriate
label binds with cDNA fragments or is incorporated when a strand is
extended for labeling of cDNA (hereinafter, such cDNA is called
labeled cDNA). Complementary binding takes place between
oligonucleotide fixed on substrate and labeled cDNA fragments.
Coordinates on substrate on which oligonucleotide are fixed, all
differ. If it is known beforehand which oligonucleotide is fixed on
which coordinates, increases or decreases in messenger RNA can be
measured simultaneously in plural numbers of genes.
[0013] In order to achieve the objective that degree of stress is
evaluated using oligonucleotide, this Inventors investigated and
found that it is necessary to place on the same array many genes,
or at least 30 or more different genes, and more desirably several
hundred DNA fragments (Oligonucleotide fragments; probe DNA). Those
genes are; (1) internal; and external standard genes for
proofreading (housekeeping genes), (2) stress-related genes such as
heat shock protein (HSP) and hormone genes such as sex hormone that
decreases under stress, (3) cytokine genes that induce immune
response and inflammatory reaction, (4) genes that induce cell
death, (5) genes related to anti-inflammation and wound healing,
and genes related to cell growth inhibition, such as
glucocorticoid, TGF.beta. and FGF, (6) transcription factor and
signaling molecules related to immune response, (7) transcription
factor and signaling molecules related to induction of cytokine,
which causes cell injury, (8) transcription factor and signaling
molecules related to growth inhibition, and (9) transcription
factor and signaling molecules related to stress response. The
above (1) to (5) are functional genes that govern specific
functions in the body, and (6) to (9) are signal transfer genes
that govern transmission of signals between functional genes.
[0014] This Inventors also found that by positioning DNA probes
that are to be fixed on substrate according to gene classification
of the above (1) to (9), results of measurement of DNA array can be
understood and evaluated immediately. In addition, this Inventors
found that by using leukocytes that are relatively easily collected
from subjects, for whom messenger RNA is tested, as specimens for
tests, degrees of stress can be easily evaluated. Thus, this
Invention was completed. Concrete means to solve problems are
explained below.
[0015] This Invention is an array on which plural oligonucleotides
with different base sequences are fixed at known, different
positions on a support medium, and the oligonucleotide array is
characterized by the fact that the said oligonucleotides are those
of genes mentioned in the above (1) to (9) or strands of
complementary sequences on the said genes, and the base sequence of
said oligonucleotides comprises bases that number at least 20 or
more.
[0016] An oligonucleotide array of this Invention also is
characterized by the fact that nucleotides are those of genes
related to mediating factors that intermediate 3 parties of the
endocrine, immune and nervous systems that are known to work in
coordination in stress reaction, or those of strands of
complementary sequences, and the base sequence of said
oligonucleotides comprises bases numbering at least 20 or more.
Examples of said mediating factors include corticotropin releasing
hormone (CRH) and cytokine.
[0017] In addition, an oligonucleotide array of this Invention is
characterized by the fact that oligonucleotides fixed on the same
support medium have the base sequence comprising bases that number
at least 20 or more, and consist of gene groups related to 2 or
more different signal transfer pathways or strand groups of
complementary sequences on said gene groups. Said gene groups
comprise at least 2 or more types of genes that code intracellular
signal transfer related protein groups that lie between cell
membrane receptors and intranuclear receptors and transcription
factors that are on the same signal transfer pathway.
[0018] Futhermore, this Invention is a gene expression analytical
method using two oligonucleotide arrays. Using the first
oligonucleotide array with plural oligonucleotides with different
base sequences that are fixed on a support medium, gene expression
analysis is conducted comprehensively to select gene groups that
show changes in the level of expression and gene groups related to
said gene groups. The second oligonucleotide array is made of
oligonucleotides of the above selected gene groups, related gene
groups and strands of complementary sequences on said selected gene
groups and related gene groups. Said oligonucleotides have the base
sequence comprising bases that number 20 or more and are fixed on a
support medium. Said second oligonucleotide array also is used for
gene expression analysis.
[0019] This invention was completed using the investigation results
on stress response mentioned above. By using the oligonucleotide
array of this invention, it is possible to easily evaluate the
degree of disorder, malfunction, symptom (stress) judging from not
only each gene but also focusing on the change of balance among the
nervous system, endocrine system and immune system. Particularly,
by arranging each gene on the substrate while taking into account
two axes such as "life and death" and "inflammation and
anti-inflammation", intuitive evaluation of the results is
possible. Also, since the oligonucleotide probes on the array of
this invention are narrowed down to those that have a deep
relationship with stress response, the number of oligonucleotide
types to be used as probes for the array are greatly reduced, thus
allowing to reduce the price. Furthermore, by fixing a single type
of oligonucleotide in several positions as a probe, the signal
intensity of multiple positions can be averaged to increase
reliability. Also, by making a rule for arranging the gene groups,
relationships between genes related to a certain disorder can be
evaluated at a glance.
[0020] Other objects, features and advantages of the invention will
become apparent from the following description of the embodiments
of the invention taken in conjunction with the accompanying
drawings.
BRIEF DESCRIPTION OF THE DRAWINGS
[0021] FIG. 1 illustrates DNA probe position on substrate (Example
1).
[0022] FIG. 2 illustrates DNA probe position on substrate (Example
2).
[0023] FIG. 3 illustrates an example of stress evaluation.
[0024] FIG. 4 illustrates an example of general structure of DNA
chip.
[0025] FIG. 5 is an example of positioning rule.
[0026] FIG. 6 illustrates an example of plural positioning on one
DNA chip substrate.
[0027] FIG. 7 illustrates an example of correlation score of
genes.
[0028] FIG. 8 illustrates an example of intergenic pathway.
[0029] FIG. 9 illustrates an example of DNA chip making kit.
[0030] FIG. 10(A) illustrates control scatter plot.
[0031] FIG. 10(B) illustrates a patient's scatter plot.
[0032] FIG. 11 illustrates an example of positioning rule.
[0033] FIG. 12 illustrates fluorescence patterns of control A to
E.
[0034] FIG. 13 illustrates a patient's fluorescence pattern.
[0035] FIG. 14 illustrates a flow chart of measurement using DNA
chip.
[0036] FIG. 15 illustrates an outline of DNA chip making using gene
positioning in Bioinformatics.
[0037] FIG. 16 illustrates a flow chart of DNA chip making using
gene positioning in Bioinformatics.
[0038] FIG. 17 illustrates an outline of DNA chip making using gene
groups positioning based on experimental results.
[0039] FIG. 18 illustrates a flow chart of DNA chip making using
gene groups positioning based on experimental results.
[0040] In the drawings, numerals represent the following:
[0041] 1. Substrate, 2. Probe DNA fixation region, 11. Probe DNA of
housekeeping genes, 12. Probe DNA of stress-tolerance and
survival-related genes and hormones, 13. Probe DNA of
inflammation-, immune response-, and cell proliferation-related
genes, 14. Probe DNA of apoptosis and cell death-inducing genes,
15. Probe DNA of gene related to anti-inflammation, wound-healing,
and cell growth inhibition, 16. Probe DNA of immune response
related transcription factors and signaling molecules, 17. Probe
DNA of cytokine inductive transcription factors and signaling
molecules, 18. Probe DNA of cell growth inhibition related
transcription factors and signaling molecules, 19. Probe DNA of
stress response related transcription factors and signaling
molecules, 20. Fluorescence detector, 21. DNA probe, 22.
Fluorescence labeled gene, 23. Supporter, 24. Example of probe
positioning according to expression pattern, 25. Gene, 26.
Correlation score, 27. Gene, 28. Inter-gene pass way, 29. Reagent,
30. Spotter, 31. Computer for controlling the spotter, 32. Chip
(being made), 33. Chip (finished), 34. Fluorescence detector, 35.
Computer for controlling the fluorescence detector, 36. Positioning
information file, 37. Public database, 38. In-house database, 39.
Network connected computer, 40, Probe stock, 41. Automatic
dispenser, 42. Probe to be spotted, 46. Experimental results, 47.
Computer for experimental data analysis.
PREFERRED EMBODIMENT OF THE INVENTION
[0042] FIG. 4 illustrates a general structure of DNA chip. FIG. 14
illustrates a flow chart of measurement using DNA chip. First, DNA
probes (21) are fixed on to a support medium (23). Gene fragments
extracted from samples obtained from subjects of measurement are
labeled with fluorescent label, etc. The fluorescent-labeled gene
(22) and DNA probes (21) are hybridized. Then, fluorescence light
originated from fluorescent label is detected by a detector (20).
Detection demonstrates the level of fluorescent-labeled gene (22)
that were hybridized with each of DNA probes (21). This is called
gene expression profile.
[0043] Oligonucleotide, that is, DNA probe, is classified according
to P value, FDD and SVD. The P value is a value called in
statistics as significant probability, which expresses degrees of
dissociation of statistics from null hypothesis in hypothesis
testing. The P value is expressed between 0 and 1. The smaller the
figure is the larger the dissociation is. The null hypothesis in
the Specification of this application is defined as "there is no
difference in the level of expression between gene A originating
RNA and gene B originating RNA." When P is 0, it means that gene A
originating RNA differs from gene B originating RNA, and when P is
1, it means that gene A originating RNA is the same as gene B
originating RNA. The P value can be obtained in, for example,
parametric tests such as t-test and F-test or non-parametric tests
such as Wilcoxon test.
[0044] Differential display is one of methods of detecting the
difference in messenger RNA that expresses in cells under different
conditions. The principle of the method is that messenger RNA that
is reverse transcribed using oligo dT primer is combined with
various primers. The combinations are amplified in PCR for
comparison of band patterns in electrophoresis in each sample. When
fluorescent labeling is used for signal detection, it is called
fluorescent differential display (FDD). Messenger RNA that
expresses can be either known or unknown.
[0045] Support vector machine (SVM) is a method based on machine
learning used for classification of hand-written letters and
images, and one of methods used to classify given data into plural
categories. SVM is an algorithm with which differences among
messenger RNA expressing in cells under different conditions are
classified. Thus, SVM is an algorithm of classification that
belongs to supervised methods. Similar methods include nearest
neighbor, discriminant analysis, neural network and classification
tree.boosting bagging. Although the Specification of this
application mentions SMV as the typical example, any classification
methods can be used.
[0046] For example in order to evaluate degrees of stress, it is
necessary to conduct highly accurate analysis of the mechanism of
function of stress response. It is clearly avoided that DNA
fragments that should have complementary binding with one kind of
genes bind with other genes (cross hybridization). It becomes
progressively difficult, as the number of genes that are fixed on a
piece of array increases. Consequently, it is extremely difficult
to eliminate completely cross hybridization among five-thousands to
several ten-thousand genes on one DNA-array for detection. It
became clear in investigation on sequence homology based on blast
algorithm that when the base length of DNA fragments used as probes
is not more than 1,000 bases, it is desirable to place less than
1,000 to 1,500 kinds of genes on one array. Therefore, if the
purpose of use of DNA array is to elucidate the mechanism of action
of stress response, it is desirable to collect the least possible
number of genes that are related to the mechanism of action of
stress response and use only these genes for array. It is not
desirable to place on array genes that are not related to stress
response, which will result in increases in cost of making probes,
leading to eventual increases in cost of oligonucleotides. In this
Invention, the number of kinds of oligonucleotides used as probes
on array can be restricted, any one kind of oligonucleotides can be
fixed as probes at plural positions. Signal intensity can be
obtained from plural positions, increasing reliability. Concrete
examples of positioning methods of gene groups are explained
below.
[0047] 1. Positioning Methods of Gene Groups Using
Bioinformatics.
[0048] 1) According to Gene Functions (Classification No. 1)
[0049] For example, gene groups are positioned as shown in FIGS. 1
and 2 in the Specification of this application. No. 11 indicates
internal and external standard genes for proofreading (housekeeping
genes), No. 12 stress and survival related genes and hormone genes,
No. 13 inflammation, immune response, cell proliferation related
genes, No. 14 apoptosis and cell death related genes, No. 15
anti-inflammation, wound-healing, cell growth inhibition related
genes, No. 16 immune response related transcription factor
signaling molecules, No. 17 cytokine inductive transcription
factor, signaling molecules, No. 18 cell growth inhibition related
transcription factor, signaling molecules, and No. 19 stress
response related transcription factor, signaling molecules. FIG. 1
illustrates an example in which the above 11 to 19 are positioned
at 9 fixed regions. FIG. 2 illustrates an example in which 11, 12
and 19, 13 and 16, 14 and 17, and 15 and 18 are positioned at 5
fixed regions.
[0050] Classification of genes into any among 11 to 19 is decided
based on terminology defined in the ontology database constructed
by the International Ontology Consortium
(http://www.geneontology.org/). Gene related ontology can be
searched on PubGene (http://www.pubgene.org), which is one of
publicly offered ontology database, or Gene Ontology (GO). The
PubGene database connects gene with ontology through textual
analysis of Medline, OMIM, etc. (refer to Tor-Kristian Jenssen et
al. A literature network of human genes for high-throughput
analysis of gene expression. Nature Genetics, vol.28, pp21-28). In
PubGene classification, HSPA1A, for example, which is a heat shock
protein (HSP), is closely associated with Heat shock protein (GO
No. 0003773) in the Functional Annotation and with transcription
(GO No. 006350) and immune response (GO No. 0006955) in the Cell
Process Annotation. Another HSP, HSPA1B, is classified to Heat
shock protein (GO No. 0003773) in the Functional Annotation and
apoptosis (GO No. 0006915) in the Cell Process Annotation.
Therefore, according to the Functional Annotation in PubGene, for
example, both HSPA1A and HSPA1B belong to the same stress related
gene, that is, heat stress protein. The two are classified to No.
12 Stress and survival-related genes and hormone genes. According
to the Cell Process Annotation in PubGene, on the other hand,
HSPA1A belongs to No. 13 Immune response related genes, and HSPA1B
to No. 14 Apoptosis and cell death related genes. Ontology in the
Functional Annotation and Cell Process Annotation in PubGene is
listed in the order of scores. Therefore, ontology with the largest
score or several numbers of ontology with relatively large scores
are selected for classification. Along with PubGene, any tool or
database can be used to search ontology based on gene names.
[0051] 2) Gene Positioning Within Fixation Regions (Classification
No. 2)
[0052] The final positioning of genes that are distributed on
fixation regions in the above 1) is decided according to any one or
the combination of two or more of the following information; (1)
gene correlation scores obtained through database, (2) information
on pairing of ligand and receptor, (3) information on
protein-protein interaction, and (4) information on gene pathway.
The list of genes contained at each fixation region is obtained in
Classification No. 1. Genes on the list are sorted out in the order
of gene names (or gene symbol names) or put in order impromptu. For
example, gene A on the top of list is fixed at the pre-determined
position, such as at the corner or center of its fixation region.
Then, genes that have strong correlation with gene A are sought.
Supposing that gene B and gene C have strong correlation with gene
A, then these two genes are positioned next to gene A. Gene B and
gene C whose positions have been decided are eliminated from the
list. Gene D, which is now at the top of the list, is positioned
where genes A, B and C are not positioned. In the same manner as
above, Gene E and gene F that have strong correlation with gene D
are sought and positioned next to gene D. By repeating the process,
genes with strong correlation with each other gather closely and
form clusters within each fixation region. Methods of how to search
for genes with strong correlations with each other are explained
below.
[0053] In the method (1) above, it is regarded that the more
frequently the two genes appear in the same sentence of the same
database, the stronger the correlation between two genes is. The
correlation score can be obtained, for example, by looking up
PubGene database (refer to Tor-Kristian Jenssen et al. A Nature
Genetics. Vol.28, pp21-28.). FIG. 7 illustrates an example. Circles
in FIGURE indicate genes, lines connecting circles the presence of
correlation between genes, and numbers along lines the correlation
scores. The correlation scores in FIG. 7 indicate the frequencies
in which two genes connected with a line are mentioned in the same
abstract in MEDLINE. Six genes that have strong correlations with
ADPRT at the center of FIG. 7 are TP53, CFTR, EEF2, FRA1H, SP1 and
ADF. Every one of 6 genes has a correlation score 1. When plural
genes have the same correlation scores, genes are sorted, for
example, in the alphabetical order and positioned around ADPRT
accordingly. When the correlation scores differ, genes are
positioned in the order of higher scores. The database used in
PubGene is MEDILINE and OMIM by the American NCBI. Database in
other references can also be used.
[0054] Positioning based on the above (2) information on pairing of
ligand and receptor means that genes which proteins have a
relationship of ligand and receptor are positioned adjacent to each
other, for example insulin-like growth factor 1 (IGF1) and
insulin-like growth factor 1 receptor (IGF1R) or insulin (INS) and
insulin receptor (INSR) are positioned adjacent to each other.
[0055] Positioning based on the above (3) information on
protein-protein interaction means that positioning of genes are
decided according to protein interaction databases such as, for
example, UCLA DIP (Database of Interacting Proteins by University
California Los Angeles, USA, refer to I.Xenarios et al. DIP: the
database of interacting proteins. Nucleic Acid Research. Vol.28,
pp.289-291, 2000). In database of interacting proteins, proteins
that interact each other are connected with lines as illustrated in
FIG. 7. The intensity of interaction can be based on bonding
strength of molecules, which can be indicated with, for example,
dissociation constant obtained in experiments. The higher the
bonding strength is, the greater the interaction intensity is. In
addition, the interaction intensity that is confirmed in plural, or
more than 2, experiments can be regarded stronger than that
confirmed in just 1 experiment. Database of protein interaction
other than DIP can be used.
[0056] Positioning based on the above (4) information on gene
pathway means that genes related to intracellular and intercellular
information transfer are positioned according to correlations in
pathway. FIG. 8 illustrates the typical pathway, that is, MAPK
(mitogen activated protein kinase) pathway. Circles indicate genes,
and arrows connecting genes indicated the directions of information
transfer between genes. For example, positioning of MEK gene
adjacent to Mos gene and positioning Raf gene and ERK gene adjacent
to MEK gene demonstrate that these genes belong to the same pathway
and genes that transfer information directly are positioned close
to each other. Other pathway information, for example, Pathway
database (http://www.biocarta.com/), can also be used. Gene
positioning can also be reflected on compiled information related
to gene relationship, such as metabolic pathway database KEGG
(http://www.kegg.kyoto.u.ad.p).
[0057] In this application, gene positioning on substrate on which
DNA chips are fixed can be decided according to gene functions
(Classification No. 1) using ontology in PubGene database, and gene
positioning within fixation regions (Classification No. 2) can be
decided based on gene correlations obtainable by searching PubGene
database. However, the contents of PubGene database change, as
information contained in literatures keeps increasing yearly.
Consequently, gene correlation scores are expected to change, every
time new findings appear. Accordingly, gene positionings on the
fixation substrate have to change based on the content of
information in literature. The positioning of DNA chips on the
fixation substrate can be decided using, aside from PubGene, any or
the combination of the following; gene interaction database based
on experimental results, such as the above DIP, signal transfer
pathway database, and metabolic pathway database. Furthermore,
database describing gene interaction that will be newly constructed
in the future.
[0058] FIG. 15 illustrates an outline of DNA chip making using gene
positioning in Bioinformatics. FIG. 16 is a flow chart of the
above. First, gene information is obtained from public database
(37) through networking such as Internet or in-house database (38).
Using methods published in this Specification based on obtained
gene information, positioning of DNA probes (21) on the support
medium (23) is decided. Positioning is processed, for example, by a
computer (39) connected to networking. Positioning of DNA probes
(21) on the support medium (23) is carried out, for example, using
a spotter (30). The positioning of DNA probes (21) on a 96- or
384-well plate (42) that houses DNA probes for spotting is
calculated backwards based on performance rules of the spotter (30)
so that the previously decided positioning of DNA probes (21) on
the support medium (23) is realized. If DNA probes are stocked in
other plates (40), the DNA probes are transferred to the above
plate (42) using a subdividing robot (41). The subdivision on the
plate (42) using a robot (41) is carried out to meet the
positioning of probes for spotting that is calculated to realize
the previously decided positioning of probes is realized on the
support medium. Finally, using the spotter (30), DNA probes (21)
housed in the plate (42) are spotted on the support medium (23) to
make DNA chips.
[0059] 2. Positioning Methods of Gene Groups Based on Experimental
Data
[0060] The above 1, demonstrates concrete examples of gene
positioning on DNA chip fixation substrate using Bioinformatics and
not based on experimental data. In this paragraph, gene positioning
methods are described based on experimental data.
[0061] 1) Data Assembling by Chips or FDD
[0062] First, 2 kinds of specimens are collected for comparison,
and RNA is extracted from each specimen. Two kinds of specimens for
comparison consist of, for example, specimens from patients with
some disease and those from healthy persons. Specimens can be any
of tissues, blood and cells that contain RNA. It is desirable for
the consideration of individual differences to collect plural
numbers of specimens, or as many as possible, from both patients
and healthy persons. Gene expression in specimens from both
subjects is analyzed using DNA chips or FDD. The DNA chip can be,
for example, cDNA chips that uses as a probe the PCR-amplified DNA
fragments using cDNA clone as template, or can be oligo chips that
are used by Aphimetrics Co. in the USA. It is desirable to have
gene probes of DNA chips as many as possible for the utmost
analysis of the state of gene expression. For example, human genes
are thought to number 30,000 to 40,000 and the transcription
products to total approximately 100,000 including alternative
splicings. Therefore, it is ideal to use DNA chips loaded with
several tens of thousands of gene probes. If it is not possible to
use DNA chips with a large number of gene probes, the state of gene
expression can be analyzed, for example, in transcription products
using FDD.
[0063] FIG. 17 illustrate an outline of DNA chip making using gene
positioning based on experimental data. FIG. 18 is a flow chart of
FIG. 17. First, experimental data are assembled in FDD method or
DNA chip method, and then, analyzed by a computer (47) to obtain
gene information. Based on the obtained gene information, the
positioning of DNA probes (21) on the support medium (23) is
decided using the published methods in the Specification of this
application. Processes following decision of the positioning are
the same as those in DNA chip making using Bioinformatics
illustrated in FIGS. 15 and 16.
[0064] 2) Gene Positioning Based on Statistical Analysis
[0065] This paragraph describes methods of positioning of DNA chips
on the fixation substrate in the Specification of this application,
which are based on the results of measurement of the state of
expression in 2 kinds of comparable specimens using DNA chip method
or FDD method described above. When each of 2 kinds of specimens
are plural, results of measurement are statistically analyzed and
used for positioning of genes on the fixation substrate. Original
data obtained in DNA chip experiments comprise the signal intensity
of the 2 kinds of comparable specimens and ratios between the
signal intensity of the 2 kinds of specimens. For example, when
specimen 1 is labeled with fluorescent dye Cy3 and specimen 2 with
Cy5, data obtained are Cy3 fluorescent intensity originated from
specimen 1, Cy5 fluorescent intensity originated from specimen 2,
and Cy3/Cy5, the ratio of fluorescent intensity.
[0066] Original data obtained in FDD experiments comprise the
intensity of bands of lanes in electrophoresis of specimen 1, that
of specimen 2, and the ratios between the intensities of bands
derived from 2 specimens. For example, when both specimens 1 and 2
are labeled with the same dye (Cy3, for example), data obtained are
Cy3 fluorescent intensity originating from specimen 1, that
originated from specimen 2, and the ratio between 2 fluorescent
intensities. Statistical analysis is conducted using (1)
fluorescent intensity ratios or (2) fluorescent intensity
originated from specimens 1 and 2.
[0067] TABLE 39 shows results of experiments using 2 kinds of
specimens that are analyzed based on the above (1) fluorescent
intensity ratios. Columns in TABLE 39 are, from the left, gene name
(symbolic name in Unigene), mean fluorescent intensity ratios,
standard deviation (SD) and CV value (SD/mean). In TABLE 39,
specimen 1 is CD3+ cell (T cell) originating from peripheral blood
of 3 healthy subjects, and specimen 2 is CD3- cell (lymphocytes
other than T cell) originating from peripheral blood of 3 healthy
subjects. Gene groups in specimens 1 and 2, the fluorescent
intensity ratio of which is 3 or higher in the state of expression,
are listed in the order of the mean value. TABLES 39 shows results
of experiments using DNA chips with several thousands genes.
Therefore, similar values can be obtained from other several
thousands genes aside from those in TABLE 39, and these genes can
be listed in the ascending or descending order of mean values, as
one pleases. In TABLE 39, the fluorescent intensity ratios in the
above (1) are those of CD3- cells/CD+ cells, and in (2) are those
of CD+ cells/CD- cells. When DNA chips are newly created, the whole
or part of several thousand gene probes can be positioned on the
DNA chip fixation substrate according to the ascending or
descending order of the mean fluorescent intensity. For example,
probes can be positioned selecting genes among several thousand
genes with the fluorescent intensity ratio 2 or higher, that is,
the difference in gene expression between specimens 1 and 2 is
twice or more.
[0068] FIG. 5 illustrates an example of the positioning rule.
Darkness of color is in proportion to the size of the mean
fluorescent intensity ratio. FIG. 5(A) illustrates an example in
which probes are positioned diagonally originating at the corner of
DNA chip substrate. FIG. 5(B) illustrates an example in which
probes are positioned concentrically originating at the center of
DNA chip substrate. FIG. 6 illustrates examples in which
positionings shown in FIG. 5 are placed side by side, or in plural
numbers, on one DNA chip substrate. FIG. 6(A) illustrates 4 of the
positioning shown in FIG. 5(A), and FIG. 6(B) illustrates 4 of the
positioning shown in FIG. 5(B). FIG. 6 corresponds to gene
positioning described in the above 1, in which genes are classified
according to functions, and the final positioning is decided based
on experimental data.
[0069] TABLE 40 shows results of experiments using 2 kinds of
specimens same to TABLE 39that are analyzed based on the above (2)
specimen 1-originating fluorescent intensity and specimen
2-originating fluorescent intensity. Columns in TABLE 40 are, from
the left hand side, gene name (symbolic name in Unigene), t value
that is statistic value obtained in t-test, and P value that is
significant probability derived from t value. Genes with P value,
or significant probability, 0.003 or lower, are listed in the
ascending order. TABLE 40 shows the results of experiments using
DNA chips with several thousands of genes. Therefore, similar
values are obtained from other several thousands of genes aside
from those in TABLE 40, and these genes can be listed in the
ascending or descending order of t value or P value, as one
pleases. When DNA chips are newly created, the whole or part of
several thousands of gene probes can be positioned on the DNA chip
fixation substrate according to the ascending or descending order
of t value or P value. Gene probes can be positioned on the DNA
chip fixation substrate in the similar way using other statistic
values obtained in testing methods other than t test, such as rank
sum test.
[0070] When DNA chips are newly created, the whole or part of
several thousands of gene probes can be positioned on the DNA chip
fixation substrate according to the ascending or descending order
of t value. For example, suppose the significant probability P is
lower than 0.2, that is, the difference in the gene expression
between specimens 1 and 2 is zero, probes can be positioned
selecting genes among several thousands of genes with the 20%
probability that the supposition is incorrect. Probe positioning
can also be decided based on results of FDD in the same process as
in TABLES 39 and 40. Aside from statistic analysis, using support
vector machine (SVM) algorithm, well known in the field of machine
learning, weight matrix factor (wi) corresponding to each gene is
obtained and probe positioning can be decided in the ascending or
descending order of wi. Probe positioning can be decided using any
method, aside from statistic analysis and machine learning, that
can rank genes based on experimental data.
[0071] As regards effects of stress on the body, various genes
related to the nervous, immune and endocrine systems are thought to
play roles. Details have been unclear. Therefore, this Inventors
investigated changes in gene expression profile in human peripheral
blood samples by creating array with a large number of genes/EST as
probes and selected genes, the expression of which changed markedly
as stress load increased. As the probes of array, 15,000 kinds of
genes/EST were purchased from IMAGE Consortium and used to create
DNA probes array for screening. Exercise stress and gastric ulcer
stress were chosen as typical stress stimulants.
[0072] With respect to exercise stress, subjects on bicycle
ergometers received for a continuous 60 minutes the load of
approximately 80% (80% VO.sub.2max) in relative value, when the
maximal individual oxygen intake (VO.sub.2max, the maximum value of
oxygen taken up by blood in unit time) is defined as 100%. When
measured in actual subjects, the 80% VO.sub.2max is approximately
180 watts at bicycle ergometer intensity. Pulse rates during
exercise were between 150 and 175/min. The lactate threshold (LT)
corresponds to approximately 60% VO.sub.2max, and heart rates
between 110 and 130/min. Therefore, the exercise load of
80%VO.sub.2max for 60 min was thought to be sufficient intensity as
exercise stress load. Peripheral blood 50 cc was collected within 5
min after the completion of exercise. Messenger RNA was extracted
from leukocyte and reverse transcribed in prescribed methods for
DNA synthesis. At reverse transcription, fluorochrome-labeled DNA
was synthesized using dCTP labeled with fluorescent dye Cy-5
(labeled cDNA: exercise stress load). Meanwhile, prior to exercise
stress load, peripheral blood 50 cc was collected from the same
subjects. Messenger RNA was extracted in the same process and
reverse transcribed using Cy-3 labeled dCTP for cDNA synthesis
(labeled cDNA: control).
[0073] Equivalent weight of labeled cDNA of exercise stress load
and that of control were mixed, placed on the above-mentioned DNA
probe array for screening, and hybridized under prescribed
conditions. After rinsing, fluorescent intensity at each spot was
measured using a laser scanner for evacuation of kinds and levels
of genes expressed in cDNA of exercise stress load and that of
control. TABLE 1 shows genes that had changes in the level of
expression more than twice, when the level of expression was
compared between the two. The increases in the level of expression
in TABLE 1 are standardized assuming that the levels of expression
of housekeeping genes, such as .beta.-actin, HPRT and GAPDH, is
stable. The level of expression of these genes is thought to be
stable under various stimulations.
[0074] Under exercise stress, the increases in the level of
expression were observed in genes related to hormones of the
hypothalamic-posterior pituitary system such as vasopressin and
anginine vasopressin, adrenocorticotropic hormone (ACTH) receptor
genes and genes related to glucocorticoids (cortisol). The level of
expression also increased in genes related to catecholamine such as
monoamine oxidase. In addition, the expression increased in
cytokine genes such as interleukin 6 (IL-6), transcription factors
such as NF-.kappa.B, and HSP70 and HSP90, heat shock proteins.
Observed also were changes in proton pump genes, that is, decreases
in Ca.sup.2+ATPase, and increases in expression of apoptosis
related genes called GADD34.
[0075] With respect to gastric ulcer stress, messenger RNA was
extracted from peripheral blood 50 cc collected from patients with
gastric ulcer, and reverse transcribed in prescribed methods for
cDNA synthesis. At reverse transcription, flurochrome-labeled cDNA
was synthesized using dCTP labeled with fluorescent dye Cy-5
(labeled cDNA: gastric ulcer stress). Meanwhile, peripheral blood
50 cc was collected from healthy subjects who do not have gastric
ulcer. Messenger RNA was extracted and reverse transcribed using
Cy-3 labeled-dCTP for cDNA synthesis in the same process. (labeled
cDNA: control).
[0076] Equivalent weight of labeled cDNA of gastric ulcer stress
and that of control were mixed, placed on the above-described DNA
probe array for screening and hybridized under prescribed
conditions. After rinsing, fluorescent intensity at each spot was
measured using a laser scanner for evaluation of kinds and levels
of gene expression in cDNA of gastric ulcer stress and that of
control. TABLE 2 shows genes that had changes in the level of
expression more than twice, when the level of expression was
compared between the two. The increases in the level of expression
in TABLE 2 are standardized assuming that the level of expression
of housekeeping genes, such as .beta.-actin, HPRT and GAPDH, is
stable. The level of expression of these genes is thought to be
stable under various stimulations.
[0077] Under gastric ulcer stress, the increases in the level of
expression were observed in genes related to hormones of the
hypothalamic-anterior pituitary system such as CRH, and genes
related to ACTH and glucocorticoid. Conversely, there were little
changes in the level of expression of genes related to hormones of
the hypothalamus-posterior pituitary system such as vasopressin.
Observed also were, as in exercise stress, increases in the
expression of cytokine genes such as IL-6 and HSP70 and HSP90, heat
shock proteins. The expression of ERK6, a signal transfer gene, and
JUN, a transcription factor, as well as anti-inflammation related
genes such as prostaglandin increased.
[0078] The above findings suggested that genes that had more than
twice increases in the level of expression, in either exercise
stress or gastric ulcer stress, included genes related to
corticotropin-releasing hormones (CRH) such as vasopressin and
oxytocin, ACTH and adrenocortical hormones such as glucocorticoid,
reflecting activation of the pituitary glands and adrenal cortex by
excitation of the hypothalamus. Hereinafter, the
hypothalamic-pituitary adrenocortical system is called HPA system.
Involvement of catecholamine related genes reflected the activation
of sympathetic adrenomedullary (SAM) system. Hormones produced by
the endocrine system such as HPA system and SAM system were
secreted into blood and bound with hormone receptors on blood
cells, increasing the expression of G-proteins and intracellular
signal transfer related genes, such as adenylatecyclase and
NF-.kappa.B. Finally, the expression of cytokine gene was induced.
The expression of stress proteins such as heat shock protein
increased as a part of stress reaction at cell level. Activation of
glucocorticoid receptor by adrenocortical hormones (glucocorticoid)
induced apoptosis in the calcium pathway. Changes in expression
occurred in the similar gene groups under 2 completely different
stresses suggested that it would be useful in analysis of complex
system of stress reaction to observe changes in the expression
intensity of these gene groups. That is to say, for analysis of
degree of stress, DNA array is the most appropriate, on which the
necessary but minimal amount of the following genes are fixed; (1)
internal and external standard genes for proofreading genes, (2)
stress resistant and survival related genes and hormone genes such
as HSP, (3) cytokine genes, (4) apoptosis and cell death r related
genes, (5) anti-inflammation and cell growth inhibition related
genes such as glucocorticoid, (6) immune response related
transcription factor or signaling molecules, (7) cell
injury-inducing cytokine inductive transcription factor or
signaling molecules, (8) cell growth inhibition related
transcription factor or signaling molecules, and (9) stress
response related transcription factor or signaling molecules.
[0079] By dividing probe fixation regions on the support medium
according to the above classification (1) to (9), persons
performing measurements are able to recognize results in patterns.
If probe fixation regions are not divided by gene functions,
processes of displaying results are required after fluorescent
signals are obtained, which include changes in positions of spots
using computer, number plotting and graph display. By classifying
probe genes according to functions and positioning said genes on
substrate according to functions, persons performing measurements
are able to judge instantly the degree of stress just by displaying
fluorescent signals on the screen. Thus, simplification of
equipment structure and lowering cost can be achieved easily.
Proofreading is necessary in order to eliminate manufacturing
variations, when plural numbers of array are created.
Oligonucleotides for proofreading are called internal and external
standard genes for proofreading. An example of internal standard
gene for proofreading is housekeeping gene. The housekeeping gene
works in coding of structural proteins and enzymes of the energy
metabolism system that are necessary for cell survival. The gene is
thought to exist in any cell with different differentiation. For
example, .beta.-actin, GAPDH, HPRT, .alpha.-tubulin, transferrin
receptor and ubiquitin are housekeeping genes. As the gene is
already present in subjects' samples such as those of leukocyte,
the gene can be the internal standard for proofreading. Internal
standard means substances that are already present in samples
without being added from outside and can be standard at
proofreading. External standard genes for proofreading are gene
sequences that are not present in humans but present in plants,
microorganisms and insects. For example, Arabidopsis thaliana gene,
plasmid DNA, bacteriophage DNA and firefly luciferase gene are
external standard. As the gene is not present in subjects' samples
such as those of leukocytes, external standard genes at known
concentrations are added to samples at the time of measurement to
be used as external standard for proofreading. External standard
means substances that are not already present in samples and added
separately from outside to be standard for proofreading.
[0080] Stress related genes are proteins that are induced at the
time of stress caused by physical and environmental factors such as
heat shock. For example, HSP, a kind of stress protein, expresses
when cells are exposed to high temperature. This HSP expresses and
increases by not only external stimulation such as exposure to high
temperature but also direct injection of denatured protein into
cells (Anathan, J. et al. Abnormal proteins serve as eukaryotic
stress signals and trigger the activation of heat shock genes.
Science, 232, 252-254, 1986). That is to say, the expression of HSP
is not induced by the bodily systems such as nervous, endocrine and
immune systems, but by changes occurring inside cells. HSP70, a
HSP, is known to have the function of inhibition of apoptosis,
which is called program cell death (Mosser, D. D. Roles of the
human heat shock protein hsp70 in protection against stress-induced
apoptosis. Mol. Cell Biol., 17, 5317-5327, 1997). Apoptosis is a
form of cell death that occurs in cells that are exposed to viral
infections, oxidation stress, radiation and anticancer drugs.
Apoptosis is induced by excessive stress on cells. HSP70 inhibits
cell death by providing cells with stress resistance. Cells in
which HSP70 expresses are not only continuously resistant to stress
that was the direct cause but also resistant to other stresses
(cross resistance), suggesting that HSP is the stress reaction
processing mechanism that cells possess. It is extremely useful to
know degrees of, or increase or decrease in, expression of stress
protein, in order to evaluate degrees of stress at the cellular
level. More than 30 kinds of stress proteins are known to exist.
Therefore, it is desirable to fix approximately 30 or more oligo
probes, including stress proteins, on the oligonucleotide array of
this Invention. Stress proteins include, for example, HSP27 (small
HSP), HSP40 (Hdj1), HSP47, HSP60/HSP10, HSC70, HSP70, mtHSP70,
HSP90, HSP100 (GRP95), HSP150 (ORP150), Bip (GRP78) and TriC.
[0081] Genes related to cell survival include, aside from stress
proteins, for example, cyclin, which regulates cell cycle, cyclin
dependent kinase (CDK), CDK inhibitors (CKI) such as cyclin A,
cyclin B, cyclin D, cyclin E, CDK1, CDK2, CDK4 and CDK6.
[0082] "Hormones" means organic compounds that are produced in
endocrine glands, secreted in blood and carried to target organs,
where microdose demonstrates specific physiological actions.
Typical endocrine systems include (a) HPA system, (b) SAM system,
(c) automatic nervous-pancreatic endocrine system, (d)
hypothalamic-sympathetic-renin angiotensin system, (e)
hypothalamic-posterior pituitary system, and (f) opioid peptide
system. Hormone-related genes include, for example, vasopressin
(AVP), vasopressin receptor (AVPR), CRH, CRH receptor (CRHR), MC2R,
REN, TH, TSHB and TSHR.
[0083] "Cytokines" are general names of bioactive peptides that
induce cell growth differentiation and are secreted by blood cells.
Cytokines differ from hormones in that cytokine works near where
they are secreted and blood concentrations of cytokines are equal
to or lower than those of hormones. Major cytokines include
granulocyte-colony stimulating factor (G-CSF), macrophage-colony
stimulating factor (M-CSF), granulocyte-macrophage colony
stimulating factor (GM-CSF), erythropoietin, thrombopoietin, stem
cell factor (SCF), interleukin-1, -2, -3, -4, -5, -6, -7, -8, -9,
-10, -11, and -12, tumor necrosis factor (TNF) and interferon.
[0084] Most of the genes with functions of inducing cell death due
to stress are thought to be apoptosis-related genes, because almost
all cell deaths in the body are those called apoptosis. Pathways
where apoptosis occurs include calcium pathway, death signal
pathway, ceramid pathway, mitochondria pathway and DNA injury
pathway. In calcium pathway, phosphatidyl-inositol-3-phosphate
receptor, calmodulin, ALG2 and carpine play roles. In death signal
pathway, TNF.alpha., Fas ligand, TRADD, FADD, RAIDD, FADD, RIP,
RAIDD, CASP8, CASP1, CASP3, TRAMP and TRAIL are known to play
roles. In ceramid pathway, stress-activated protein kinase
(SAPK)/Jun terminal-N kinase (JNK) plays a role. In mitochondria
pathway, Bcl-2 associated X protein (Bax2), Bcl-2, Bcl-xL, and
caspase gene play roles. In DNA injury pathway, p53, p21, p51, p73
and MDM2 genes play roles. Genes related to anti-inflammation such
as glucocorticoid and genes related to growth inhibition include
cytochrome P450 gene 11B1 (CYP11B1), CYP11B2, CYP17, CYP21A2,
glucocorticoid modulatory element binding protein (GMEB),
glucocorticoid receptor repression factor (GRLF), myocilin (MYOC),
glucocorticoid receptor .alpha. (NR3C1), proopiomelanocortin (POMC)
and prostaglandin G/H synthase precursor.
[0085] Transcription factors and signaling molecules related to
immune response, cytokine induction, growth inhibition and stress
resistance include, for example, ATF/CREB transcription factor,
NF-.kappa.B transcription factor, JUN gene and 14-3-3n gene. In
most signal transfers, signals are generally transferred in the
mechanism that protein is activated by chemical change of
phosphorylation and the activated protein in turn induces
phosphorylation of the adjacent protein, and so forth. Signal
transfer pathways are called pathways, which are generally
differentiated by naming with representative proteins on pathways
(Nomenclature is referred to www.biocarta.com) Known are, for
example, MAPK (mitogen activated protein kinase), ATM (ataxia
telangiectasia mutated), BCR (B cell receptor), CD40 (related to
tumor necrosis factor receptor), CXCR4 (related to chemokine
receptor), EGF (epidermal growth factor), EPO (erythropoietin), FAS
(fatty-acyl-CoA synthase), FcEpsilon (Fc fragment of IgE receptor),
IFN (interferon) alpha, IFN (interferon) gamma, IGF-1 (insulin-like
growth factor-1), IL (interleukin)-2, -3, -4, -5, -6, and -18,
NF.kappa.B (nuclear factor .kappa.B), NCF (nerve growth factor),
p53 , PDGF (platelet derived growth factor), PLC (phospholipase C),
SODD (silencer of death domains), TCR (T cell receptor), TGF.beta.
(transforming growth factor .beta.), TNFR1 (tumor necrosis factor
receptor 1), TNFR2 (tumor necrosis factor receptor 2), TPO
(thrombopoietin), and Wnt (wingless/int-1). By placing genes that
work in coding of proteins that are keys of these pathways on array
as probes, signal transfer pathways induced by stress stimulation
can be identified. In particular, for patients with chronic stress,
which is caused due to dysfunction of one of the proteins on the
signal transfer pathway, treatment plans can be determined by
identifying the site where signal transfer is interrupted.
[0086] Another example of DNA chip is described, in which
oligonucleotides are placed in such a way so that the presence or
absence of stress can be understood instantly. This example of
practice is one of the examples of gene positioning based on
experimental data.
[0087] One week before and 5 hours after an examination, peripheral
blood 10 cc was collected from one person (patient A) who became
excessively tense during examination and 5 persons (control A, B,
C, D and E) who did not feel much tension during the same
examination. Total RNA was extracted from lymphocytes from both
groups. Degrees of stress of patient A, who experienced excessive
tension and 5 controls were significantly different in tests by
interview conducted by a specialist. Tests by interview confirmed
that 5 persons who did not feel excessive tension were not in the
state of stress. In experiments with DNA chip housing several
thousands genes, the state of expression 1 week before examination
was compared with that 5 hours after examination in control A to E.
The difference in the state of expression was small between the
two. Correlation (R.sup.2) between fluorescent intensity before
examination and that after examination was 0.94 to 0.97. FIG. 10(A)
shows scatter plot of control A. Correlation of the same sample is
0.99. Therefore, values 0.94 to 0.97 indicate that the state of
expression before examination did not differ greatly from that
after examination. The means of fluorescent intensity ratios with
several thousands of genes were obtained in control A to E and
listed in ascending order. Then, gene probes were positioned
originating at the right upper corner of chip substrate toward the
left lower corner following the rules of FIG. 11. Each square of
FIG. 11 is the position where gene probes are fixed. Numbers in
squares indicate that genes are positioned following the direction
of arrows in FIG. 11 in the order of size of the fluorescent
intensity ratio (Cy5/Cy3). The positioning of FIG. 11 shows that
genes with large Cy5/Cy3 are concentrated and fixed at the right
upper portion and genes with large Cy3/Cy5 at the left lower
portion. FIG. 12 shows patterns obtained following measurement of
RNA by DNA chip in FIG. 11 in 5 controls, A to E. In FIG. 12, the
greater the change in the gene expression, or the greater the ratio
Cy5/Cy3 or Cy3/Cy5 is, the darker the gene is. FIGS. 12(A) to 12(E)
illustrate patterns of control A to E. In all five, the patters are
similar, or the right upper and left lower portions have dark
circles and the intermediate is light. FIG. 13 shows the pattern
obtained in measurement in patient A using DNAA chip in FIG. 11. In
FIG. 13, the right upper and left lower portions have fewer dark
circles. The differences between the 2 figures are instantly
recognizable. The correlation (R.sup.2) between fluorescent
intensity before and after examination in patient A was 0.88 (see
FIG. 10(B)), which is apparently different from that in 5 controls
and the differences are demonstrated in FIGS. 12 and 13.
[0088] In order to place the oligonucleotides with the sequence of
the above-described genes as probes on the array, it is necessary
to decide which parts of the gene sequences are the probes. What
must be taken into consideration at that time are melting
temperature (Tm) and cross hybridization. In order to carry out
highly accurate and highly stringent hybridization between DNA
fragments fixed on the DNA array and DNA fragments originating from
samples, the relationship is important between hybridization
temperature (Th) and Tm of fixed DNA fragment. It is necessary that
the difference between the Tm of fixed DNA fragments and the Th
does not exceed 30.degree. C. Cross hybridization occurs when there
is high homology among DNA sequences. Therefore, in order to
prevent cross hybridization from occurring, it is necessary that
any of fixed DNA fragments and sample-originated DNA fragments have
low homology with DNA fragments that do not hybridize originally
with fixed DNA fragments. Furthermore, it is desirable that these
DNA fragments do not contain portions that have high homology with
sequences with mini hair pin structure or repetitive sequence that
is known in human genes as Alu sequence. It is also necessary to
calculate the homology not only between gene sequences fixed on one
piece of array but also between DNA sequences and gene sequences of
species listed on GENBANK etc. It is desirable not to select DNA
sequences for fixed DNA fragments that have high homology with DNA
sequences of gene groups that are possibly contained in samples to
be measured.
[0089] DNA fragments to be fixed as probes can be synthesized in
PCR reaction using commercially available cDNA library as template.
Oligonucleotide array can be created from synthesized DNA fragments
by preparing prescribed concentrations (0.1 to 1.0 .mu.G/.mu.L),
and spotting using a spotter on slide glasses that are already
coated with polylysine or aminosilane. Degrees of stress are
studied using the above-described oligonucleotide array in the
following procedure. First, peripheral blood samples are collected
from several volunteers who do not have stress symptoms, and
messenger RNA is extracted from leukocytes. For example, a
messenger RNA pool of average healthy people can be obtained by
mixing messenger RNA from many persons. This messenger RNA pool is
described hereinafter in the Specification of this application as
Universal Control. Next, peripheral blood samples are collected
from test subjects, and messenger RNA is extracted from leukocytes.
With messenger RNA of peripheral blood of test subjects, labeled
cDNA is synthesized using Cy5-dCTP in reverse transcription using
oligo dT primer. With messenger RNA in Universal control, labeled
cDNA is synthesized using Cy3-dCTP. Test subjects' cDNA (Cy5
labeled) and Universal control cDNA (Cy3 labeled) are mixed and
placed on the same, above-described oligonucleotide array for
hybridization at prescribed temperature and duration. It is
desirable to have hybridization temperature between 45.degree. C.
and 70.degree. C., and time between 6 and 18 hours. Following
hybridization, fluorescent intensity of Cy5 and Cy3 at each site
where genes are spotted is measured using a fluorescent scanner and
compared for the difference in the level of expression. Extraction
of messenger RNA is performed with either monocytes, which account
for 3 to 7% of leukocytes, or lymphocytes, which account for 25 to
33%. Analysis can be expected to reflect better the degrees of
stress, because the monocyte has capability to differentiate to
macrophage, which is an important cell in the natural immune
system, and the lymphocyte to T cell and B cell, which are
important cells in the acquired immune system. In addition, these
leukocytes have difference cell rotation (dynamics) including
maturation in bone marrow, retention time in peripheral blood and
life duration. Therefore, it is possible to evaluate acute
bioresponse using polynuclear leukocytes (neutrophil), short-term
reaction using monocytes and relatively long-term bioresponse using
lymphocytes.
[0090] Below is an example in which changes in degrees of stress in
daily activities were studied in one subject.
[0091] The 793 genes (TABLE 3 and TABLE 38) were selected from
GENBANK Unigene by way of key words retrieval, etc. based on the
rationale described in the above "Summary of the Invention". These
genes work in coding of (1) internal and external standard genes
for proofreading, (2) stress resistance and survival related genes
such as HSP and hormone genes, (3) cytokine genes, (4) apoptosis
and cell death related genes, (5) anti-inflammation related genes
such as glucocorticoid and cell growth inhibition related genes,
(6) immune response related transcription factor and signaling
molecules, (7) cell injury inducing cytokine inductive
transcription factor and signaling molecules, (8) cell growth
inhibition related transcription factor and signaling molecules,
and (9) stress response related transcription factor and signaling
molecules.
[0092] Next, 793 oligonucleotide probes with highly specific and
similar Tm were designed following algorithm consisting of the
following procedures; 1. Reading of gene sequence files, 2. Input
of salt concentrations and experimental conditions at
hybridization, 3. Input of length of fixed DNA fragments, 4.
Calculation of melting temperature (Tm) of fixed DNA fragments,
followed by elimination from lists of candidates of DNA fragments
whose melting temperature does not meet a certain range of Tm, 5.
Elimination from the candidate lists of DNA fragments with specific
superorganization or repetitive sequences, 6. Elimination from the
candidate lists of DNA fragments with high homology with repetitive
sequences such as Alu sequence, and 7. Elimination from the
candidate lists of DNA fragments with high homology with other gene
sequences. Each of the designed 793 sequences were synthesized
using an oligonucleotide synthesizer. The total 796 kinds
oligonucleotides comprising the above 793 human gene probes and 3
kinds of oligonucleotide sequences that are not present in humans
(lambda DNA, pUC18 plasmid DNA and M13mp18DNA) and are added as
external standard genes for proofreading were fixed on a glass
substrate in the method published below.
[0093] First, commercially available slide glasses (manufactured by
Gold Seal Brand) were soaked at room temperature for 2 hours in
alkaline solution (sodium hydroxide; 50 g, distilled water; 150 ml
and 95% ethanol; 200 ml). The slide glasses were transferred to
distilled water for rinsing three times to remove alkaline solution
completely. The rinsed slide glasses were soaked for 1 hour in
10%poly-L-lysine solution (manufactured by Sigma), pulled out of
solution and centrifuged at 500 rpm for 1 min in a centrifuge for
microtiter plate to remove poly-L-lysine solution. The slide
glasses were placed in suction incubator for drying at 40.degree.
C. for 5 minutes. Amino group was introduced on the slide glasses.
The slide glasses with amino group were soaked for 2 hours in 1 mM
GMBS (by PIERCE) dimethyl sulfoxide solution and rinsed with
dimethyl sulfoxide. Maleamide group was introduced on the surface
of the slide glasses. Using a DNA synthesizer (manufactured by
Applied Biosystem, model 394), oligonucleotides to which thiol
group was introduced were synthesized, and purified in high
performance liquid chromatography (HPLC). Next, 1 .mu.l of 2 .mu.M
synthesized purified oligonucleotides, 4 .mu.L of HEPES buffer
(N-2-hydroxyethylpiperazine-N, -2-ethane sulfonic acid; 10 mM, pH
6.5), and 5 .mu.l of additive (ethylene glycol) were mixed to make
spotting solution. The prepared spotting solution was spotted
randomly on slide glasses using a spotter (manufactured by Hitachi
Soft, SPB10 2000). The slide glasses were left at room temperature
to fix oligonucleotides on slide glasses.
[0094] At that time, with the intention that persons performing
measurements can instantly recognize and judge results on the
array, probes were fixed in the positions that were published in
FIG. 1 or FIG. 2. Probe positioning was carried out based on the
above-described gene classification (1) to (9).
[0095] Peripheral blood 50 cc was collected from a test subject who
sat up for 3 nights immediately after the sit-up completed.
Immediately, messenger RNA was extracted from leukocytes and
preserved at -80.degree. C. Peripheral blood 50 cc was collected
from the same test subject after a good rest for 1 week. Messenger
RNA was extracted in the same manner. From messenger RNA obtained
immediately after sit-up, Cy5-labeld cDNA was synthesized in
reverse transcription using Cy5-dCTP. From messenger RNA obtained
after good rest, Cy3-labeled cDNA was synthesized in reverse
transcription using Cy3-dCTP.
[0096] Equivalent weight of Cy5-labed cDNA and Cy3-labeled cDNA
were mixed, placed on the above-described oligonucleotide array for
hybridization at 62.degree. C. for 2 hours. After rinsing, the
fluorescent intensity at each spot was measured using a scanner
(manufactured by GSI-Lumonics, ScanArray 5000). FIG. 3 shows an
image after measurement. Fixed probes were positioned as shown in
FIG. 2. The greater the ratio of Cy5 fluorescent intensity/Cy3
fluorescent intensity (sit-up/rest) was, the darker the circle was
in FIG. 3. It is known by experience that immune intensity lowers
due to loss of sleep. FIG. 3 demonstrates that many genes related
to inflammation and cell death related genes in FIG. 2 expressed,
suggesting that sitting up for 3 nights resulted in acute malaise,
inducing the expression of genes in immune system and apoptosis.
The expression of part of stress resistance genes such as HSP
increased as a part of stress response. Concerning gene groups
related to diseases other than stress.
[0097] Cancer can be diagnosed by using DNA chips on which genes
that play major roles in cancerization, infiltration and metastasis
such as cancer genes, cancer inhibition genes, growth factor,
transcription factor, cytokine, apoptosis, cell cycle modulator and
DNA repair genes are fixed. Particularly, by positioning at
opposites to each other on the support medium the probes that
hybridize with cancer genes and probes that hybridize with
transcription products of cancer inhibition genes, it will become
easier to recognize instantly the correlation between cancer genes
and cancer inhibition genes.
[0098] Methods of Evaluation
[0099] Method for Labeling RNA to Produce cDNA
[0100] From the total RNA or messenger RNA extracted from cells and
tissues, cDNA is synthesized in transcription reaction originating
at primer such as oligo-dT primer using transcription enzymes. At
the DNA synthesis, for example, fluorescent labels are taken up by
cDNA by adding to solution deoxynucleotides to which fluorescent
dyes such as Cy3-dCTP, Cy3-dUTP, Cy5-dCTP and Cy5-dUTP are bound.
By hybridizing the fluorescent-labeled cDNA with probes fixed on
the DNA ship substrate, RNA profile of genes can be measured using
the level of fluorescence.
[0101] When the level of the total RNA or messenger RNA in cells
and tissues is low, labeling is performed using RNA amplification.
Amplifications include, for example, T7 or SP3 amplification using
T7 or SP3 polymerase reaction. In T7 amplification, transcription
originates at T7dT primer that has T7 sequence and a sequence with
several tens of T bases. T7 sequence is present at the terminal of
synthesized cDNA in reverse transcription. Synthesis of RNA that is
complementary on cDNA and recognizes this T7 sequence is called in
vitro transcription using T7. RNA can be amplified several tens to
several hundreds times in in vitro transcription.
Fluorescent-labeled cDNA can be synthesized using RNA obtained in
this RNA amplification in the same method described above as
synthesis of cDNA labeled with RNA. By hybridizing this
fluorescent-labeled cDNA with probes fixed on the DNA chip
substrate, RNA profile of genes can be measured by the level of
fluorescence.
[0102] Manufacturing Methods of Chip
[0103] When oligonucleotide groups are positioned on the DNA chip
using a spotter, it is necessary to house beforehand
oligonucleotide group in a 96- or 384-well plate. Positioning of
wells of the 96- or 384-well plate on coordinates on the DNA chip
is determined by how a spotter is set up. When the positioning on
the DNA chip is already determined based on Bioinformatics or
experimental data as in the Specification of this application, it
is necessary to establish the housing positions of oligonucleotide
groups on a 96- or 384-well plate according to the establishment of
the spotter. Conventionally, the position of oligonucleotide groups
on the DNA chip was established according to the housing position
of oligonucleotide groups in a 96-well plate. In the Specification
of this application, conversely, the housing position of
oligonucleotide groups on a 96-well plate is established according
to the position of oligonucleotide groups on the DNA chip.
[0104] Methods of Display
[0105] 1. Real Display
[0106] The value of fluorescent intensity of Cy5 and Cy3 labeling
are displayed in quasi-color according to the intensity. In another
quasi-color display, red indicates Cy5 labeling and green Cy3
labeling. On quasi-color images, boarder lines that divide plural
sections can be overlapped for display. It is possible to convert
images in left and right, or top and bottom inversions and
rotation. Graphic displays with bars are possible according to the
fluorescent intensity. Three-dimensional bar graphs can be
displayed corresponding to the probe fixation positions.
[0107] 2. Virtual Display
[0108] More than 2 DNA chips can be displayed on one piece. For
example, using quasi-colors, the mean value of each probe, the
largeness of standard deviation, correlation between one probe and
another probe can be displayed in the order of the size of
correlation. Repositioning can be displayed based on information of
probe positions already registered on computer.
[0109] DNA Chip Making Kit
[0110] DNA chip making kit can be offered, which is not a completed
DNA kit but a partially completed one. For example, as shown in
FIG. 9, a kit containing a set consisting of substrate for DNA
fixation, basic probe set, positioning information on basic probe
set, spotter and computer can be offered. Because of being
partially completed, in addition to the basic probe set offered as
a kit, new probes can be added as the user desires. The user inputs
information on gene functions and the state of expression of added
probes. Thus, classification of gene functions and the state of
expression housed in positioning information of the basic probe set
merge to classification of gene functions and the state of
expression of added probe set. Real display and virtual display are
materialized on computer screen based on the merged classification
of gene functions and the state of expression.
[0111] As described above, degrees of stress can be evaluated by
using the array of this Invention. It is thought that various
changes in and close interaction among the three systems or the
nervous, endocrine and immune systems lead to complex stress
reaction. Conventional methods of measurement of specific hormones
in blood are only measuring the endocrine system, but ignoring the
interactions among the three, the nervous, endocrine and immune
systems. Consequently, it is difficult to find the correlation
between hormone level and degrees of stress in conventional methods
because of the individual differences in hormone level and other
reasons. In view of defects of conventional methods, this Invention
took notice of not only changes in each of the nervous, endocrine
and immune systems but also interactions among the three systems,
particularly the balance in the interactions. Thus, this Invention
was achieved.
[0112] It should be further understood by those skilled in the art
that the foregoing description has been made on embodiments of the
invention and that various changes and modifications may be made in
the invention without departing from the spirit of the invention
and the scope of the appended claims.
[0113] For example, other aspects of this invention are as
follows:
[0114] (11) A method of displaying results of label detection of
hybridization wherein labeled cell-derived RNA are hybridized to an
oligonucleotide array comprising multiple subblock regions and
oligonucleotides with different base sequences positioned to each
of said multiple subblock regions, wherein said oligonucleotides
are positioned according to an arrangement pattern wherein
oligonucleotides with a first correlation degree are positioned
closer to each other than oligonucleotides that have a lower
correlation degree; and results of label detection of said
hybridization are displayed.
[0115] (12) A method of displaying results of label detection of
hybridization wherein labeled cell-derived RNA are hybridized to an
oligonucleotide array comprising multiple subblock regions and
oligonucleotides with different base sequences positioned to each
of said multiple subblock regions, wherein said oligonucleotides
are positioned according to an arrangement pattern wherein
oligonucleotides with a first correlation degree are positioned
closer to each other than oligonucleotides that have a lower
correlation degree; and results of label detection of said
hybridization are rearranged on a screen with determined
correlation between oligonucleotides.
[0116] (13) A kit for fabrication of an oligonucleotide array
comprising multiple subblock regions and oligonucleotides with
different base sequences positioned to each of said multiple
subblock regions, wherein said oligonucleotides are positioned
according to an arrangement pattern wherein oligonucleotides with a
first correlation value are positioned closer to each other than
oligonucleotides that have a lower correlation value, wherein said
kit comprises an oligonucleotide fixation substrate, fixation
probes, probe positioning information, a spotter to spot said
probes, a monitor screen to display addressing information of the
spotter and detection results, or a computer with a monitor that
determined the correlation value are provided.
1TABLE 1 GenkBank Name of gene M14758 P-glycoprotein (PGY1) mRNA
(MDR1) M25647 vasopressin mRNA; Arginine vasopressin NM_000707
arginine vasopressin receptor 1B Z11687 antidiuretic hormone
receptor NM_001402 eukaryotic translation elongation factor 1 alpha
1 U83981 Homo sapiens apoptosis associated protein (GADD34)
NM_006582 glucocorticoid modulatory element binding protein 1
AB034989 KIAA0025 gene product M69177 Human monoamine oxidase B
J04027 ATPase, Ca++ transporting, plasma membrane 1 NM_002415
macrophage migration inhibitory factor NM_000261 Homo sapiens
myocilin M14584 Human interleukin 6 mRNA NM_001078 Homo sapiens
vascular cell adhesion molecule 1 NM_005345 heat shock 70kD protein
1 M58603 Human nuclear factor kappa-B DNA binding subunit p105
M34664 Heat shock 60kD protein 1 AF028832 Heat shock 90kD protein
1, alpha
[0117]
2TABLE 2 GenkBank Name of gene AF022224 Bcl-2-binding protein
NM_004244 CD163 antigen U82812 scavenger receptor cysteine rich Sp
alpha U47741 CREB-binding protein X58022 corticotropin-releasing
factor binding protein NM_001402 eukaryotic translation elongation
factor 1 alpha 1 NM_000862 hydroxy-delta-5-steroid dehydrogenase, 3
beta- and steroid delta-isomerase 1 NM_002228 v-jun avian sarcoma
virus 17 oncogene homolog (JUN) mRNA M14584 Human interleukin 6
mRNA X79483 ERK6 mRNA for extracellular signal regulated kinase
NM_000529 melanocortin 2 receptor (adrenocorticotropic hormone)
NM_001043 solute carrier family 6 member 2 (SLC6A2) M59979
prostaglandin G/H synthase 1 precursor X54079 Heat shock 27kD
protein 1 D90224 glycoprotein 34 (gp34) NM_005345 heat shock 70kD
protein 1 AF028832 Heat shock 90kD protein 1, alpha
[0118]
3TABLE 3 M14758 Homo sapiens P-glycoprotein (PGY1) mRNA (MDR1)
M14752 V-abl Abelson murine leukemia viral oncogene homolog 1
NM_000789 Homo sapiens dipeptidyl carboxypeptidase 1 (angiotensin I
converting enzyme) (ACE) X00351 cytoplasmic beta-actin (ACTB)
L17075 Human TGF-b superfamily receptor type I mRNA; activin
receptor-like kinase 1 (ACVRL1; ALK1) U92649 Homo sapiens snake
venom-like protease (cSVP) mRNA, A disintegrin and
metalloproteinase domain 17 (tumor necrosis factor, alpha,
converting enzyme) L05500 Homo sapiens adenylate cyclase 1 (ADCY1);
Human fetal brain adenylyl cyclase mRNA, 3' end AF070583 Homo
sapiens clone 24648 adenylyl cyclase mRNA, partial cds NM_004036
Homo sapiens adenylate cyclase 3 (ADCY3) AF250226 Homo sapiens
adenylyl cyclase type VI mRNA NM_001114 Homo sapiens adenylate
cyclase 7 (ADCY7) Z35309 H. sapiens mRNA for adenylyl cyclase
NM_001116 Homo sapiens adenylate cyclase 9 (ADCY9) NM_001117 Homo
sapiens adenylate cyclase activating polypeptide 1 (pituitary)
(ADCYAP1) NM_001118 Homo sapiens adenylate cyclase activating
polypeptide 1 (pituitary) receptor type I (ADCYAP1R1) M18112 Human
poly (ADP-ribose) polymerase mRNA (ADPRT), PARP M87290 Human
angiotensin II type 1 receptor mRNA X65699 H. sapiens mRNA for
angiotensin II receptor NM_000686 Homo sapiens angiotensin receptor
2 (AGTR2) NM_005161 Homo sapiens angiotensin receptor-like 1
(AGTRL1) NM_005162 Homo sapiens angiotensin receptor-like 2
(AGTRL2) NM_003488 Homo sapiens A kinase (PRKA) anchor protein 1
(AKAP1) NM_007202 Homo sapiens A kinase (PRKA) anchor protein 10
(AKAP10) AB014529 A kinase (PRKA) anchor protein 11 (AKAP11); Homo
sapiens mRNA for KIAA0629 protein, partial cds NM_005100 Homo
sapiens A kinase (PRKA) anchor protein (gravin) 12 (AKAP12)
NM_007203 Homo sapiens A kinase (PRKA) anchor protein 2 (AKAP2)
NM_006422 Homo sapiens A kinase (PRKA) anchor protein 3 (AKAP3)
NM_003886 Homo sapiens A kinase (PRKA) anchor protein 4 (AKAP4)
NM_004857 Homo sapiens A kinase (PRKA) anchor protein 5 (AKAP5)
[0119]
4TABLE 4 NM_004274 Homo sapiens A kinase (PRKA) anchor protein 6
(AKAP6) NM_016377 Homo sapiens A kinase (PRKA) anchor protein 7
(AKAP7) NM_005858 Homo sapiens A kinase (PRKA) anchor protein 8
(AKAP8) NM_005751 Homo sapiens A kinase (PRKA) anchor protein
(yotiao) 9 (AKAP9) M63167 Human rac protein kinase alpha mRNA
(akt1), complete cds NM_001283 Homo sapiens AP1S1adaptor-related
protein complex 1, sigma 1 subunit (AP1S1) NM_003916 Homo sapiens
adaptor-related protein complex 1, sigma 2 subunit (AP1S2) AF013263
Homo sapiens apoptotic protease activating factor 1 (Apaf- 1) mRNA,
complete cds M74088 adenomatous polyposis coli protein (APC
protein); DP2.5 AB023421 Homo sapiens mRNA for heat shock protein
apg-1; Heat shock protein (hsp110 family) U45879 Human inhibitor of
apoptosis protein 2 mRNA; Apoptosis inhibitor 1 U45878 Human
inhibitor of apoptosis protein 1 mRNA; Apoptosis inhibitor 2 X06820
H. sapiens rhoB gene mRNA; Ras homolog gene family, member B L25081
Homo sapiens GTPase (rhoC) mRNA, complete cds; Ras homolog gene
family, member C X95282 H. sapiens mRNA for Rho8 protein; Ras
homolog gene family, member E X61587 H. sapiens rhoG mRNA for
GTPase; Ras homolog gene family, member G (rho G) U02570 Human
CDC42 GTPase-activating protein mRNA, partial cds X78817 H. sapiens
partial C1 mRNA; Rho GTPase activating protein 4 U17032 Human
p190-B (p190-B) mRNA, complete cds; Rho GTPase activating protein 5
AF177663 Homo sapiens GTPase-activating protein 6 isoform 4
(ARHGAP6) mRNA, alternatively spliced, complete cds; Rho GTPase
activating protein 6 NM_015366 Homo sapiens Rho GTPase activating
protein 8 (ARHGAP8), mRNA
[0120]
5TABLE 5 X69550 H. sapiens mRNA for rho GDP-dissociation Inhibitor
1 L20688 Human GDP-dissociation inhibitor protein (Ly-GDI) mRNA,
D4-GDI U82532 Homo sapiens GDI-dissociation inhibitor RhoGDIgamma
mRNA, complete cds; Rho GDP dissociation inhibitor (GDI) gamma
U64105 Human guanine nucleotide exchange factor p115-RhoGEF mRNA,
partial cds; Rho guanine nucleotide exchange factor (GEF) 1 Z35227
H. sapiens TTF mRNA for small G protein; Ras homolog gene family,
member H U96750 Homo sapiens putative tumor supressor NOEY2 mRNA;
Ras homolog gene family, member I NM_005171 Homo sapiens activating
transcription factor 1 (ATF1) M31630 Human cyclic AMP response
element-binding protein (HB16) mRNA, 3' end L19871 Human activating
transcription factor 3 (ATF3) mRNA NM_001675 Homo sapiens
activating transcription factor 4 (tax- responsive enhancer element
B67) (ATF4) NM_012068 Homo sapiens activating transcription factor
5 (ATF5) NM_007348 Homo sapiens activating transcription factor 6
(ATF6) NM_006856 Homo sapiens activating transcription factor 7
(ATF7) U33841 Human ataxia telangiectasia (ATM) mRNA M25647 Human
vasopressin mRNA; Arginine vasopressin (neurophysin II,
antidiuretic hormone, diabetes insipidus, neurohypophyseal) L25615
Human arginine vasopressin receptor 1 (AVPR1) mRNA, complete cds
NM_000707 Homo sapiens arginine vasopressin receptor 1B (AVPR1B),
mRNA Z11687 H. sapiens mRNA for antidiuretic hormone receptor;
Arginine vasopressin receptor 2 (nephrogenic diabetes insipidus)
AF009674 Homo sapiens axin (AXIN1) ,partial cds NM_004655 Homo
sapiens axin 2 (conductin, axil) (AXIN2), mRNA U66879 Human Bcl-2
binding component 6 (bbc6) mRNA; BAD protein AF022224 Homo sapiens
Bcl-2-binding protein (BAG-1) mRNA AF111116 Homo sapiens silencer
of death domains (SODD) mRNA; BCL2-associated athanogene 4
NM_017450 Homo sapiens BAI1-associated protein 2 (BAIAP2),
transcript variant 1, mRNA U23765 Human bcl2 homologous
antagonist/killer (BAK) L22474 Human Bax beta mRNA, apoptosis
regulator bax U29680 Human A1 protein; BCL-2-related protein A1
(BCL2A1); BFL1 protein
[0121]
6TABLE 6 Z23115 H. sapiens bcl-xL mRNA; BCL2-like 1 U59747 Human
apoptosis regulator bclw; KIAA0271; BCL2L2 U34584 Human Bcl-2
interacting killer (BIK); NBK apoptotic inducer protein; BP4; BIP1
U14680 Human breast and ovarian cancer susceptibility (BRCA1)
X58957 H. sapiens atk mRNA for agammaglobulinaemia tyrosine kinase
Y14153 Homo sapiens mRNA for beta-transducin repeat containing
protein (beta-TrCP) X83703 H. sapiens mRNA for cytokine inducible
nuclear protein; Cardiac ankyrin repeat protein U13699 Human
interleukin 1-beta converting enzyme isoform delta (IL1BCE) mRNA
U60519 Human apoptotic cysteine protease Mch4 (Mch4) mRNA, complete
cds U13021 Human positive regulator of programmed cell death ICH-1L
(Ich-1) mRNA, complete cds U13737 Human cysteine protease CPP32
isoform alpha mRNA, complete cds U28014 Human cysteine protease
(ICErel-II) mRNA, complete cds U28015 Human cysteine protease
(ICErel-III) mRNA, complete cds U20536 Human cysteine protease Mch2
isoform alpha (Mch2) mRNA, complete cds U37448 Human Mch3 isoform
alpha (Mch3) mRNA, complete cds U60520 Human apoptotic cysteine
protease Mch5 isoform alpha (Mch5) mRNA, complete cds U60521 Human
protease proMch6 (Mch6) mRNA, complete cds U66838 Human cyclin A1
mRNA, complete cds X51688 Human mRNA for cyclin A; Cyclin A2 M25753
Human cyclin B mRNA, 3' end.; Cyclin B1 AF002822 Human cyclin B2
mRNA, complete cds M74091 Human cyclin mRNA M64349 Human
G1/S-specific cyclin D1 (CCND1); cyclin PRAD1; bcl-1 oncogene
[0122]
7TABLE 7 M90813 Human D-type cyclin (CCND2) mRNA, complete cds;
cyclin D2 M92287 Homo sapiens cyclin D3 (CCND3) mRNA, complete cds
M73812 Human cyclin E mRNA sequence U47413 Human cyclin G1 mRNA,
complete cds U47414 Human cyclin G2 mRNA, complete cds U11791 Human
cyclin H mRNA, complete cds D50310 Human mRNA for cyclin I,
complete cds U28694 Human eosinophil CC chemokine receptor 3 mRNA,
complete cds U54994 Human CC chemokine receptor 5 (CCR5) mRNA,
complete cds NM_004244 Homo sapiens CD163 antigen (CD163) M14362
Human T-cell surface antigen CD2 (T11) mRNA, complete cds J02988
Human T-cell-specific homodimer surface protein CD28 mRNA, complete
cds NM_000732 Homo sapiens CD3D antigen, delta polypeptide (TiT3
complex) (CD3D), mRNA X03884 Human mRNA for T3 epsilon chain (20K)
of T-cell receptor (from peripheral blood lymphocytes). X04145
Human mRNA for T-cell receptor T3 gamma polypeptide, RON alpha
J04132 Human T cell receptor zeta-chain mRNA, complete cds M12807
Human T-cell surface glycoprotein T4 mRNA, complete cds M59040 CD44
antigen (homing function and Indian blood group system) U82812
Human scavenger receptor cysteine rich Sp alpha mRNA M80462 Human
MB-1 mRNA; CD79A antigen (immunoglobulin-associated alpha) M89957
Human immunoglobulin superfamily member B cell receptor complex
cell surface glycoprotein (IGB) mRNA, CD79B M27533 CD80 antigen
(CD28 antigen ligand 1, B7-1 antigen) U04343 Human CD86 antigen
mRNA, complete cds M12828 Homo sapiens T-cell surface protein T8
mRNA M36712 Human T lymphocyte surface glycoprotein (CD8-beta)
mRNA, complete cds S72008 hCDC10 = CDC10 homolog [human, fetal
lung, mRNA, 2314 nt]. U18291 Human CDC16Hs mRNA, complete cds
X05360 Human CDC2 gene involved in Cell Cycle control; CDK1 M81933
Human cdc25A mRNA, complete cds M81934 Human cdc25B mRNA, complete
cds. M34065 Human cdc25Hs mRNA, complete cds
[0123]
8TABLE 8 U00001 Human homologue of S. pombe nuc2+ and A. nidulans
bimA; Cell division cycle 27 AF067524 Homo sapiens PITSLRE protein
kinase beta SV12 isoform (CDC2L2) mRNA, complete cds M80629 Human
cdc2-related protein kinase (CHED) mRNA; Cell division cycle 2-like
5 (cholinesterase-related cell division controller) L22005 Human
ubiquitin conjugating enzyme mRNA, partial cds; Cell division cycle
34 U63131 Human CDC37 homolog mRNA, complete cds M35543 Human
GTP-binding protein (G25K) mRNA, complete cds AF022109 Homo sapiens
HsCdc18p (HsCdc18) mRNA, complete cds L33264 Homo sapiens
CDC2-related protein kinase (PISSLRE) mRNA; Cyclin-dependent kinase
(CDC2-like) 10 M68520 Human cdc2-related protein kinase mRNA,
complete cds X66357 H. sapiens mRNA cdk3 for serine/threonine
protein kinase M14505 Human (clone PSK-J3) cyclin-dependent protein
kinase mRNA; cyclin-dependent kinase 4 (CDK4) X66364 H. sapiens
mRNA PSSALRE for serine/threonine protein kinase. X80343 H. sapiens
p35 mRNA for regulatory subunit of cdk5 kinase U34051 Human
cyclin-dependent kinase 5 activator isoform p39i mRNA, complete
cds. X66365 H. sapiens mRNA PLSTIRE for serine/ threonine protein
kinase X77743 H. sapiens CDK activating kinase mRNA X85753 Homo
sapiens mRNA for CDK8 protein kinase. L25676 Homo sapiens
CDC2-related kinase (PITALRE) mRNA, complete cds L25610 Homo
sapiens cyclin-dependent kinase inhibitor mRNA; melanoma
differentiation-associated protein 6 (MDA6); CDK-interacting
protein 1 (CIP1); WAF1; p21
[0124]
9TABLE 9 NM_004064 Homo sapiens cyclin-dependent kinase inhibitor
1B (p27, Kip1), (CDKN1B) mRNA U22398 Human Cdk-inhibitor p57KIP2
(KIP2) mRNA, complete cds L27211 Human CDK4-inhibitor (p16-INK4)
mRNA; cyclin-dependent kinase 4 inhibitor (CDK4I; CDKN2); multiple
tumor suppressor 1 (MTS1); p16 U17075 Human p14-CDK inhibitor mRNA,
complete cds.; p15 AF041248 Homo sapiens cyclin-dependent kinase
inhibitor (CDKN2C) mRNA, complete cds.; p18 U40343 Human CDK
inhibitor p19INK4d mRNA, complete cds; p19 NM_005194 Homo sapiens
CCAAT/enhancer binding protein (C/EBP), beta (CEBPB) mRNA; NF-IL6
AF010127 Homo sapiens Casper mRNA; CASP8 and FADD-like apoptosis
regulator; I-FLICE AF016582 checkpoint kinase 1 (CHK1) AF009225
Homo sapiens IkB kinase alpha subunit (IKK alpha) mRNA, complete
cds; IKK1 L29222 Homo sapiens clk1 mRNA; CDC-like kinase 1 L29216
Homo sapiens clk2 mRNA; CDC-like kinase 2 L29220 Homo sapiens clk3
mRNA; CDC-like kinase 3 M58525 Homo sapiens
catechol-O-methyltransferase (COMT) mRNA NM_001873 Homo sapiens
carboxypeptidase E (CPE) Y00816 Complement component (3b/4b)
receptor 1, including Knops blood group system; CD35 M26004
Complement component (3d/Epstein Barr virus) receptor 2; CD21
U84388 Human death domain containing protein CRADD mRNA; CASP2 and
RIPK1 domain containing adaptor with death domain NM_004379 Homo
sapiens cAMP responsive element binding protein 1 (CREB1) U47741
Human CREB-binding protein (CBP) mRNA, complete cds U47741 Human
CREB-binding protein (CBP) mRNA, complete cds NM_000756 Homo
sapiens corticotropin releasing hormone (CRH), mRNA. X58022 Human
mRNA for corticotropin-releasing factor binding protein (CRF-BP).
L23332 Human corticotropin releasing factor receptor mRNA U34587
Human corticotropin-releasing factor receptor 2 mRNA U33286 Human
chromosome segregation gene homolog CAS mRNA, Chromosome
segregation 1 (yeast homolog)-like
[0125]
10TABLE 10 M37435 Human macrophage-specific colony-stimulating
factor (CSF-1) mRNA, complete cds M10663 Human T-cell
granulocyte-macrophage colony stimulating factor (GM-CSF) mRNA
M73832 Human GM-CSF receptor (GM-CSF receptor) mRNA, complete cds
M59941 Human GM-CSF receptor beta chain mRNA; IL3R-beta X03438
Human mRNA for granulocyte colony-stimulating factor (G-CSF).
M59818 Human granulocyte colony-stimulating factor receptor (G-
CSFR-1) mRNA, complete cds NM_001317 Homo sapiens chorionic
somatomammotropin hormone 1 (placental lactogen) (CSH1) mRNA V00573
Human mRNA encoding placental lactogen hormone L37042 Homo sapiens
casein kinase I alpha isoform (CSNK1A1) mRNA M55265 Human casein
kinase II alpha subunit mRNA, complete cds. M55268 Human casein
kinase II alpha' subunit mRNA, complete cds X16312 Human mRNA for
phosvitin/casein kinase II beta subunit M92934 Human connective
tissue growth factor (CTGF) X87838 H. sapiens mRNA for beta-catenin
U96136 Homo sapiens delta-catenin mRNA, complete cds, Arm L06797
Human (clone L5) orphan G protein-coupled receptor mRNA, complete
cds; Chemokine (C-X-C motif), receptor 4 (fusin) NM_000497 Homo
sapiens cytochrome P450, subfamily XIB (steroid
11-beta-hydroxylase), polypeptide 1 (CYP11B1), mRNA. NM_000498 Homo
sapiens cytochrome P450, subfamily XIB (steroid
11-beta-hydroxylase), polypeptide 2 (CYP11B2) mRNA. M14564 Human
cytochrome P450c17 (steroid 17-alpha- hydroxylase/17,20 lyase)
mRNA, complete cds. M17252 Human cytochrome P450c21 mRNA, 3' end
U18321 Human ionizing radiation resistance conferring protein mRNA;
Death associated protein 3 X76104 H. sapiens DAP-kinase mRNA
AF015956 Homo sapiens Fas-binding protein Daxx mRNA, complete cds
NM_000787 Dopamine beta-hydroxylase (dopamine
beta-monooxygenase)
[0126]
11TABLE 11 M76180 Dopa decarboxylase (aromatic L-amino acid
decarboxylase) AB029497 Homo sapiens gadd153 mRNA for CHOP
alternatively spliced isoform (CASIS) U91985 Human DNA
fragmentation factor-45 mRNA, DFF AF241254 Homo sapiens angiotensin
converting enzyme-like protein mRNA M60278 Human heparin-binding
EGF-like growth factor mRNA (HBEGF); diphtheria toxin receptor
(DTR) x68277 H. sapiens CL 100 mRNA for protein tyrosine
phosphatase, Dual specificity phosphatase 1, MKP1 U46461 Human
dishevelled homolog (DVL) mRNA, complete cds. NM_004422 Homo
sapiens dishevelled 2 (homologous to Drosophila dsh) (DVL2), mRNA
U49262 Human dishevelled (DVL) mRNA, complete cds M96577 Homo
sapiens (E2F-1) pRB-binding protein mRNA; retinoblastoma-binding
protein 3 (RBBP3); NM_001402 Homo sapiens eukaryotic translation
elongation factor 1 alpha 1 (EEF1A1) x04571 Human mRNA for kidney
epidermal growth factor (EGF) precursor; urogastrone U01877 Human
p300 protein mRNA, complete cds X02157 Human mRNA for fetal
erythropoietin M60459 Human erythropoietin receptor mRNA, complete
cds U24231 Human Fas-associating death domain-containing protein
mRNA AJ271408 Homo sapiens mRNA for Fas-associated factor, FAF1
X06948 Human mRNA for high affinity IgE receptor alpha-subunit
(FcERI); Fc fragment of IgE, high affinity I, receptor for; alpha
polypeptide M33195 Human Fc-epsilon-receptor gamma-chain mRNA; Fc
fragment of IgE, high affinity I, receptor for; gamma polypeptide
M28696 Fc fragment of IgG, low affinity IIb, receptor for (CD32)
X51943 acidic fibroblast growth factor (AFGF) + heparin-binding
growth factor 1 precursor (HBGF-1); U67918 Human keratinocyte
growth factor 2 mRNA, complete cds U66199 Human fibroblast growth
factor homologous factor 3 (FHF- 3) mRNA, complete cds U66197 Human
fibroblast growth factor homologous factor 1 (FHF- 1) mRNA,
complete cds U66198 Human fibroblast growth factor homologous
factor 2 (FHF- 2) mRNA, complete cds
[0127]
12TABLE 12 U66200 Human fibroblast growth factor homologous factor
4 (FHF- 4) mRNA, complete cds M27968 Human basic fibroblast growth
factor (FGF) mRNA (BFGF; FGFB; FGF2) M17446 Human Kaposi's sarcoma
oncogene fibroblast growth factor mRNA, complete cds M37825 Human
fibroblast growth factor-5 (FGF-5) mRNA, complete cds X63454 Human
fibroblast growth factor 6 precursor (FGF6); HBGF6; HST2 M60828
Human keratinocyte growth factor mRNA; fibroblast growth factor 7
(FGF-7) U36223 Human fibroblast growth factor 8 (FGF8);
androgen-induced growth factor precursor (AIGF); HBGF8 D14838 Human
mRNA for FGF-9 M34641 Human fibroblast growth factor (FGF)
receptor-1 mRNA M80634 Human keratinocyte growth factor receptor
mRNA; fibroblast growth factor receptor 2 (FGFR2) M58051 Human
fibroblast growth factor receptor (FGFR3) mRNA L03840 Human
fibroblast growth factor receptor 4 (FGFR4) mRNA, complete cds.
Y12863 Homo sapiens mRNA for growth factor FIGF; C-fos induced
growth factor (VEGF D) U01134 Human soluble vascular endothelial
cell growth factor receptor (sflt) mRNA; vascular endothelial
growth factor receptor 1 (VEGFR1); U02687 Human growth factor
receptor tyrosine kinase (STK-1) mRNA; FLK2 X69878 H. sapiens Flt4
mRNA for transmembrane tyrosine kinase; vascular endothelial growth
factor receptor 3 precursor (VEGFR3) X16707 Human fra-1 mRNA;
FOS-like antigen-1 NM_005479 Homo sapiens frequently rearranged in
advanced T-cell lymphomas (FRAT1) mRNA NM_000510 Homo sapiens
follicle stimulating hormone, beta polypeptide (FSHB) M65085 Human
follicle stimulating hormone receptor mRNA AB017363 Homo sapiens
mRNA for frizzled-1, complete cds X02492 Human interferon-inducible
mRNA fragment (cDNA 6-16). M32865 Human Ku protein subunit mRNA;
Thyroid autoantigen 70kD (Ku antigen) U83981 Homo sapiens apoptosis
associated protein (GADD34) mRNA M60974 Human growth arrest and
DNA-damage-inducible protein (gadd45) mRNA
[0128]
13TABLE 13 NM_015675 Homo sapiens growth arrest and
DNA-damage-inducible, beta (GADD45B) NM_006705 Homo sapiens growth
arrest and DNA-damage-inducible, gamma (GADD45G) X01677 liver
glyceraldehyde 3-phosphate dehydrogenase (GAPDH) NM_000805 Homo
sapiens gastrin (GAS) J04040 Human glucagon mRNA, complete cds
L20316 Human glucagon receptor mRNA NM_000515 Homo sapiens growth
hormone 1 (GH1) M38451 Human placenta-specific growth hormone mRNA
NM_000163 Homo sapiens growth hormone receptor (GHR) NM_000823 Homo
sapiens growth hormone releasing hormone receptor (GHRHR) NM_004122
Homo sapiens growth hormone secretagogue receptor (GHSR) NM_006582
Homo sapiens glucocorticoid modulatory element binding protein 1
(GMEB1) NM_012384 Homo sapiens glucocorticoid modulatory element
binding protein 2 (GMEB2) M69013 Human guanine nucleotide-binding
regulatory protein (G-y- alpha) mRNA; Guanine nucleotide binding
protein (G protein), alpha 11 (Gq class) L22075 Human guanine
nucleotide regulatory protein (G13) mRNA; Guanine nucleotide
binding protein (G protein), alpha 13 NM_004297 Homo sapiens
guanine nucleotide-binding protein 14 (GNA14) mRNA M63904 Human
G-alpha 16 protein mRNA, complete cds; Guanine nucleotide binding
protein (G protein), alpha 15 (Gq class) X04526 Human liver mRNA
for beta-subunit signal transducing proteins Gs/Gi (beta-G);
Guanine nucleotide binding protein (G protein), beta polypeptide 1
M16538 Human signal-transducing guanine nucleotide-binding
regulatory (G) protein beta subunit mRNA; Guanine nucleotide
binding protein (G protein), beta polypeptide 2 M24194 Human MHC
protein homologous to chicken B complex protein mRNA; Guanine
nucleotide binding protein (G protein), beta polypeptide 2-like 1
M31328 Human guanine nucleotide-binding protein beta-3 subunit
mRNA; Guanine nucleotide binding protein (G protein), beta
polypeptide 3
[0129]
14TABLE 14 AF017656 Homo sapiens G protein beta 5 subunit mRNA;
Guanine nucleotide binding protein (G protein), beta 5 U31383 Human
G protein gamma-10 subunit mRNA; Guanine nucleotide binding protein
10 U31384 Human G protein gamma-11 subunit mRNA; Guanine nucleotide
binding protein 11 NM_012202 Homo sapiens guanine nucleotide
binding protein (G protein), gamma 3 (GNG3), mRNA AF052149 Homo
sapiens clone 24733 mRNA sequence; Guanine nucleotide binding
protein (G protein), gamma 3, linked U31382 Human G protein gamma-4
subunit mRNA; Guanine nucleotide binding protein 4 AF038955 Homo
sapiens G protein gamma 5 subunit mRNA; Guanine nucleotide binding
protein (G protein), gamma 5 AB010414 Homo sapiens mRNA for
G-protein gamma 7; Guanine nucleotide binding protein (G protein),
gamma 7 S62027 transducin gamma subunit; Guanine nucleotide binding
protein (G protein), gamma transducing activity polypeptide 1
X01059 Human placenta mRNA for luteinizing hormone releasing
hormone precursor (LHRH). NM_005311 Homo sapiens growth factor
receptor-bound protein 10 (GRB10), mRNA M96995 Homo sapiens
epidermal growth factor receptor-binding protein GRB2 (EGFRBP-GRB2)
mRNA sequence M73077 Human glucocorticoid receptor repression
factor 1 (GRF-1) mRNA X12510 Human mRNA for melanoma growth
stimulatory activity (MGSA), groucho X53799 Human mRNA for
macrophage inflammatory protein-2alpha (MIP2alpha,; GRO2 oncogene
L33801 Human protein kinase mRNA; glycogen synthase kinase 3 beta
(GSK3 beta); tau kinase subunit; factor A X17644 Human GST1-Hs mRNA
for GTP-binding protein; G1 to S phase transition 1 AF250138
Protein kinase H11; Homo sapiens small stress protein-like protein
HSP22 mRNA D49742 Human mRNA for HGF activator like protein
(hyaluronan- binding protein 2) D50405 Human mRNA for RPD3 protein,
Histone deacetylase 1 D16431 Human mRNA for hepatoma-derived growth
factor, complete cds
[0130]
15TABLE 15 M60718 Human hepatocyte growth factor mRNA (HGF);
scatter factor (SF); hepatopoeitin A D14012 Human mRNA for
hepatocyte growth factor (HGF) activator precursor U51004 Homo
sapiens protein kinase C inhibitor (PKCI-1) mRNA, Histidine triad
nucleotide-binding protein X58536 Human mRNA for HLA class I locus
C heavy chain K01171 Human HLA-DR alpha-chain mRNA; Class II MHC
alpha X02902 Human mRNA for HLA class II DR-beta 1 (Dw14); Class II
MHC beta M11867 Human MHC class II HLA DR5 DR-beta-chain mRNA,
complete cds U40992 Homo sapiens heat shock protein hsp40 homolog
mRNA, complete cds; DnaJ-like heat shock protein 40
[0131]
16TABLE 16 V00530 Human hypoxanthine-guanine
phosphoribosyltransferase (HPRT) IMP: pyrophosphate
phosphoribosyltransferase U76376 Homo sapiens activator of
apoptosis Hrk (HRK) mRNA; Harakiri, BCL2-interacting protein
(contains only BH3 domain) AF068754 Homo sapiens heat shock factor
binding protein 1 HSBP1 mRNA; Heat shock factor binding protein 1
AF088982 Homo sapiens heat shock protein hsp40-3 mRNA; Heat shock
cognate 40 NM_000196 Homo sapiens hydroxysteroid (11-beta)
dehydrogenase 2 (HSD11B2) NM_000862 Homo sapiens
hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid
delta-isomerase 1 (HSD3B1) M64673 Human heat shock factor 1 (TCF5)
mRNA, complete cds; Heat shock transcription factor 1 M65217 Human
heat shock factor 2 (HSF2) mRNA, complete cds; Heat shock
transcription factor 2 AB007131 Homo sapiens mRNA for HSF2BP; Heat
shock transcription factor 2 binding protein D87673 Homo sapiens
mRNA for heat shock transcription factor 4; Heat shock
transcription factor 4 X63368 H. sapiens HSJ1 mRNA; Heat shock
protein, neuronal DNAJ- like 1 L08069 Human heat shock protein, E.
coli DnaJ homologue mRNA, complete cds; Heat shock protein,
DNAJ-like 2 AB003333 Molecular cloning, expression and localization
of human 105kDa heat shock protein, hsp105D NM_006597 Homo sapiens
heat shock 70kD protein 10 (HSC71) (HSPA10), mRNA NM_005345 Homo
sapiens heat shock 70kD protein 1 (HSPA1A), mRNA; Heat shock 70kD
protein 1 NM_005346 Homo sapiens heat shock 70kD protein 1
(HSPA1B), mRNA D85730 Homo sapiens HSPA1L mRNA for Heat shock
protein 70 testis variant, complete cds; Heat shock 70kD
protein-like 1 U56725 Human heat shock protein mRNA, complete cds;
Heat shock 70kD protein 2 L12723 Human heat shock protein 70
(hsp70) mRNA; Heat shock 70kD protein 4 X87949 H. sapiens mRNA for
BiP protein; Heat shock 70kD protein 5 (glucose-regulated protein,
78kD) X51758 Human mRNA for heat shock protein HSP70B'; Heat shock
70kD protein 6
[0132]
17TABLE 17 L15189 Homo sapiens mitochondrial HSP75 mRNA; Heat shock
70kD protein 9B (mortalin-2) X54079 Human mRNA for heat shock
protein HSP27; Heat shock 27kD protein 1 D89617 Homo sapiens mRNA
for MKBP; Heat shock 27kD protein 2 U15590 Homo sapiens heat shock
17kD protein 3 (HSPB3) mRNA, complete cds; Heat shock 27kD protein
3 AJ243191 Homo sapiens mRNA for cardiovascular heat shock protein;
Heat shock 27kD protein family, member 7 (cardiovascular) AF028832
Homo sapiens Hsp89-alpha-delta-N mRNA; Heat shock 90kD protein 1,
alpha M16660 Human 90-kDa heat-shock protein gene, cDNA; Heat shock
90kD protein 1, beta M34664 Heat shock 60kD protein 1 (chaperonin)
U07550 Human chaperonin 10 mRNA; Heat shock 10kD protein 1 D49547
Human mRNA for heat-shock protein 40; Heat shock 40kD protein 1
AF012106 Homo sapiens DnaJ protein (HSPF2) mRNA, complete cds; Heat
shock 40kD protein 2 J03132 Human intercellular adhesion molecule-1
(ICAM-1) mRNA, CD54 M91196 Homo sapiens DNA-binding protein mRNA
(Interferon consensus sequence binding protein 1) NM_005531 Homo
sapiens interferon, gamma-inducible protein 16 (IFI16) mRNA X67325
H. sapiens p27 mRNA (interferon, alpha-inducible protein 27) J03909
Human gamma-interferon-inducible protein (IP-30) mRNA, complete cds
X03557 Human mRNA for 56-KDa protein induced by interferon AF083470
Homo sapiens interferon induced tetratricopeptide protein IFI60
(IFIT4) mRNA, complete cds J04164 Human interferon-inducible
protein 9-27 mRNA, complete cds X57351 Human 1-8D gene from
interferon-inducible gene family X57352 Human 1-8U gene from
interferon-inducible gene family V00551 Messenger RNA for human
leukocyte (alpha) interferon V00538 Messenger RNA for human
leukocyte (alpha) interferon V00542 Messenger RNA for human
leukocyte (alpha) interferon M28585 Human leukocyte
interferon-alpha mRNA, complete cds, clone pIFN105 M54886 Human
interferon-alpha mRNA, complete cds V00540 Messenger RNA for human
leukocyte (alpha) interferon V00541 Messenger RNA for human
leukocyte interferon (one of eight). V00550 Messenger RNA for human
leukocyte (alpha) interferon.
[0133]
18TABLE 18 J03171 Human interferon-a1pha receptor (HuIFN-alpha-Rec)
mRNA, complete cds X77722 H. sapiens mRNA for interferon alpha/beta
receptor V00547 Human messenger RNA for fibroblast (beta)
interferon X13274 Human mRNA for interferon IFN-gamma J03143 Human
interferon-gamma receptor mRNA, complete cds U05875 Human clone
pSK1 interferon gamma receptor accessory factor-1 (AF-1) mRNA,
complete cds X02669 Human mRNA for type 1 interferon-omega 1.
Y08915 Immunoglobulin (CD79A) binding protein 1 X57025 Human IGF-I
mRNA for insulin-like growth factor I X04434 Human mRNA for
insulin-like growth factor I receptor J03242 Human insulin-like
growth factor II mRNA, complete cds J03528 Human cation-independent
mannose 6-phosphate receptor mRNA; insulin-like growth factor II
receptor M31145 Human insulin-like growth factor binding protein
mRNA, complete cds M35410 Human insulin-like growth factor binding
protein 2 (IGFBP2) mRNA M31159 Human growth hormone-dependent
insulin-like growth factor-binding protein mRNA, complete cds
M62403 Human insulin-like growth factor binding protein 4 (IGFBP4)
mRNA, complete cds AF055033 Homo sapiens clone 24645 insulin-like
growth factor binding protein 5 (IGFBP5) mRNA, complete cds M62402
Human insulin-like growth factor binding protein 6 (IGFBP6) mRNA,
complete cds S75725 prostacyclin-stimulating factor [human,
cultured diploid fibroblastcells, mRNA, 1124 nt]. AF044195 Homo
sapiens IkappaB kinase complex associated protein (IKAP) mRNA,
complete cds; IKKAP2 AF080158 Homo sapiens IkB kinase-b (IKK-beta)
mRNA, IKK2/beta; IKK2 AF074382 Homo sapiens IkB kinase gamma
subunit (IKK-gamma) mRNA, NLK M57627 Human interleukin 10 (IL10)
mRNA, complete cds U00672 Human interleukin-10 receptor mRNA,
complete cds Z17227 Homo sapiens mRNA for transmebrane receptor
protein M57765 Human interleukin 11 mRNA, complete cds
[0134]
19TABLE 19 Z38102 H. sapiens mRNA for interleukin-11 receptor
M65291 Human natural killer cell stimulatory factor (NKSF) mRNA,
complete cds, clone p35 M65290 Human natural killer cell
stimulatory factor (NKSF) mRNA, complete cds, clone p40 U03187
Human IL12 receptor component mRNA, complete cds U64198 Human I1-12
receptor beta2 mRNA, complete cds L06801 Homo sapiens interleukin
13 mRNA, complete cds Y09328 H. sapiens mRNA for IL13 receptor
alpha-1 chain U70981 Human interleukin-13 receptor mRNA, complete
cds AF070546 Homo sapiens clone 24607 mRNA sequence AF031167 Homo
sapiens interleukin 15 precursor (IL-15) mRNA, complete cds. U31628
Human interleukin-15 receptor alpha chain precursor (IL15RA) mRNA,
complete cds M90391 Homo sapiens putative IL-16 protein precursor,
mRNA, complete cds NM_014443 Homo sapiens interleukin 17B (IL17B),
mRNA NM_013278 Homo sapiens interleukin 17C (IL17C), mRNA U58917
Homo sapiens IL-17 receptor mRNA, complete cds D49950 Homo sapiens
mRNA for interferon-gamma inducing factor(IGIF), complete cds
AB019504 Homo sapiens mRNA for interleukin-18 binding protein,
complete cds U43672 Human putative transmembrane receptor IL-1Rrp
mRNA, complete cds NM_013371 Homo sapiens interleukin 19 (IL19),
mRNA X02531 Human mRNA for interleukin 1-alpha M15330 Human
interleukin 1-beta (IL1B) mRNA, complete cds M27492 Human
interleukin 1 receptor mRNA, complete cds X59770 H. sapiens IL-1R2
mRNA for type II interleukin-1 receptor, (cell line CB23). D12763
Homo sapiens mRNA for ST2 protein
[0135]
20TABLE 20 U49065 Human interleukin-1 receptor-related protein
mRNA, complete cds X53296 H. sapiens mRNA for IRAP V00564 Human
mRNA encoding interleukin-2 (IL-2) a lymphozyte regulatory molecule
X01057 Human mRNA for interleukin-2 receptor M26062 Human
interleukin 2 receptor beta chain (p70-75) mRNA, complete cds
D11086 Human mRNA for interleukin 2 receptor gamma chain M17115
Human multilineage-colony-stimulating factor mRNA, complete cds
M74782 Human interleukin 3 receptor (hIL-3Ra) mRNA, complete cds
M13982 Human interleukin 4 (IL-4) mRNA, complete cds X52425 Human
IL-4-R mRNA for the interleukin 4 receptor X04688 Human mRNA for
T-cell replacing factor (interleukin-5). M75914 Human interleukin 5
receptor alpha mRNA, complete cds M14584 Human interleukin 6 mRNA,
complete cds X12830 Human mRNA for interleukin-6 (IL-6) receptor
M57230 Human membrane glycoprotein gp130 mRNA, Interleukin 6 signal
transducer (oncostatin M receptor) J04156 Human interleukin 7
(IL-7) mRNA, complete cds M29696 Human interleukin-7 receptor
(IL-7) mRNA, complete cds M17017 Human beta-thromboglobulin-like
protein mRNA, complete cds L19591 Homo sapiens interleukin 8
receptor alpha (IL8RA) mRNA, complete cds L19593 Homo sapiens
interleukin 8 receptor beta (IL8RB) mRNA, complete cds M30134 Human
P40 protein mRNA, complete cds M84747 Human interleukin 9 receptor
mRNA, complete cds. U58198 Human interleukin enhancer binding
factor 3 mRNA X60787 Human mRNA for transcription factor ILF U10323
Human nuclear factor NF45 mRNA, complete cds U10324 Human nuclear
factor NF90 mRNA, complete cds AF001954 Homo sapiens growth
inhibitor p33ING1 (ING1) mRNA, complete cds NM_001564 Homo sapiens
inhibitor of growth family, member 1-like (ING1L) mRNA NM_000207
Homo sapiens insulin (INS), mRNA NM_005542 Homo sapiens insulin
induced gene 1 (INSIG1) NM_000208 Homo sapiens insulin receptor
(INSR), mRNA. M10051 Human insulin receptor mRNA, complete cds
J05046 Human insulin receptor-related receptor (IRR) mRNA, 3' end
NM_000209 Homo sapiens insulin promoter factor 1, homeodomain
transcription factor (IPF1)
[0136]
21TABLE 21 L76191 Homo sapiens interleukin-1 receptor-associated
kinase (IRAK) mRNA, complete cds AF026273 Homo sapiens
interleukin-1 receptor-associated kinase-2 mRNA, complete cds
X14454 Human mRNA for interferon regulatory factor 1 X15949 Human
mRNA for interferon regulatory factor-2 (IRF-2). Z56281 H. sapiens
mRNA for interferon regulatory factor 3 U52682 Human lymphocyte
specific interferon regulatory factor/interferon regulatory factor
4 (LSIRF/IRF4) mRNA, complete cds U51127 Human interferon
regulatory factor 5 (Humirf5) mRNA, complete cds AF027292 Homo
sapiens interferon regulatory factor 6 (IRF6) mRNA, complete cds
U53830 Homo sapiens interferon regulatory factor 7A mRNA, complete
cds S62539 insulin receptor substrate-1 [human, skeletal muscle,
mRNA, 5828 nt]. S62539 insulin receptor substrate-1 [human,
skeletal muscle, mRNA, 5828 nt]. NM_003749 Homo sapiens insulin
receptor substrate 2 (IRS2) NM_003604 Homo sapiens insulin receptor
substrate 4 (IRS4) M13755 Human interferon-induced 17-kDa/15-kDa
protein mRNA (interferon-stimulated protein, 15 kDa) U88964 Human
HEM45 mRNA, complete cds M87503 Human IFN-responsive transcription
factor subunit mRNA; Interferon-stimulated transcription factor 3,
gamma (48 kD) ; p48
[0137]
22TABLE 22 L12002 Human integrin alpha 4 subunit mRNA, complete
cds; Integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA- 4
receptor) Y00796 Human mRNA for leukocyte-associated molecule-1
alpha subunit (LFA-1 alpha subunit)., CD11a J03925 Integrin, alpha
M (complement component receptor 3, alpha; also known as CD11b
(p170), macrophage antigen alpha polypeptide) X07979 Integrin, beta
1 (fibronectin receptor, beta polypeptide, antigen CD29 includes
MDF2, MSK12); M15395 Human leukocyte adhesion protein
(LFA-1/Mac-1/p150, 95 family) beta subunit mRNA, CD18 AF049893 Homo
sapiens insulin upstream factor 1 (IUF1) mRNA M64174 Human
protein-tyrosine kinase (JAK1) mRNA, Janus kinase 1 AF005216 Homo
sapiens receptor-associated tyrosine kinase (JAK2) mRNA, Janus
kinase 2 U09607 Human JAK family protein tyrosine kinase (JAK3)
mRNA, complete cds NM_002228 Homo sapiens v-jun avian sarcoma virus
17 oncogene homolog (JUN) mRNA. K00558 human alpha-tubulin mRNA,
complete cds AF039597 Ku86 autoantigen related protein 1 X61656 H.
sapiens mRNA for growth factor receptor tyrosine kinase; Kinase
insert domain receptor (a type III receptor tyrosine kinase)
AB034989 KIAA0025 gene product; MMS-inducible gene; Homo sapiens
mRNA for stress protein Herp D23673 Human mRNA, clone HH109
(screened by the monoclonal antibody of insulin receptor
substrate-1 (IRS-1)). M59964 Human stem cell factor mRNA; (SCF);
mast cell growth factor (MGF); c-kit ligand (KITLG) AF036905 Homo
sapiens linker for activation of T cells (LAT) mRNA M36881 Human
lymphocyte-specific protein tyrosine kinase (lck) mRNA NM_000894
Homo sapiens luteinizing hormone beta polypeptide (LHB) M73746 Homo
sapiens lutropin/choriogonadotropin receptor (LHCGR) mRNA M13451
Human lamin C mRNA, complete cds, Lamin A M34458 Human lamin B
mRNA, complete cds, M94362 Human lamin B2 (LAMB2) mRNA, partial cds
NM_016103 Homo sapiens GTP-binding protein Sara (LOC51128), mRNA
AF125392 Homo sapiens insulin induced protein 2 mRNA, complete cds
AF119666 Homo sapiens insulin receptor tyrosine kinase substrate
mRNA
[0138]
23TABLE 23 D12614 Human mRNA for lymphotoxin (TNF-beta), complete
cds U77352 Homo sapiens MAP kinase-activating death domain protein
(MADD) mRNA U68018 Human mad protein homolog (hMAD-2) mRNA;
JV18-1.MADR2 OR SMAD2 U68019 Homo sapiens mad protein homolog
(hMAD-3) mRNA, complete cds U44378 Human homozygous deletion target
in pancreatic carcinoma (DPC4); mothers against dpp homolog 4
(SMAD4) AF035528 Homo sapiens Smad6 mRNA, complete cds AF010193
Homo sapiens MAD-related gene SMAD7 (SMAD7) mRNA, complete cds
NM_000240 Homo sapiens monoamine oxidase A (MAOA), nuclear gene
encoding mitochondrial protein, mRNA M69177 Human monoamine oxidase
B (MAOB) mRNA, complete cds L11284 Homo sapiens ERK activator
kinase (MEK1) mRNA L11285 Homo sapiens ERK activator kinase (MEK2)
mRNA D87116 Human mRNA for MAP kinase kinase 3b, complete cds, MEK3
U17743 Human JNK activating kinase (JNKK1) mRNA, complete cds; SEK1
U39064 Human MAP kinase kinase 6 mRNA, complete cds; MEK6 AF013588
Homo sapiens mitogen-activated protein kinase kinase 7 (MKK7) mRNA,
complete cds AF042838 Homo sapiens MEK kinase 1 (MEKK1) mRNA,
partial cds Y10256 H. sapiens mRNA for serine/threonine protein
kinase, NIK NM_003188 Homo sapiens mitogen-activated protein kinase
kinase kinase 7 (MAP3K7), mRNA, TAK1 AF096300 Homo sapiens
HPK/GCK-like kinase HGK mRNA, complete cds M84489 Human
extracellular signal-regulated kinase 2 mRNA; ERK2 U92268 Homo
sapiens mitogen activated protein kinase p38-2 mRNA, complete cds
X79483 H. sapiens ERK6 mRNA for extracellular signal regulated
kinase X79483 H. sapiens ERK6 mRNA for extracellular signal
regulated kinase AF004709 Homo sapiens stress-activated protein
kinase 4 (SAPK4) mRNA, complete cds
[0139]
24TABLE 24 L35253 Human p38 mitogen activated protein (MAP) kinase
mRNA; cytokine suppressive anti-inflammatory drug binding protein
(CSAID binding protein; CSBP); MAX-interacting protein 2 (MXI2)
L35253 Human p38 mitogen activated protein (MAP) kinase mRNA;
cytokine suppressive anti-inflammatory drug binding protein (CSAID
binding protein; CSBP); MAX-interacting protein 2 (MXI2) X60188
Human ERK1 mRNA for protein serine/threonine kinase L26318 Human
protein kinase (JNK1) mRNA; SAPK X60287 H. sapiens max mRNA
NM_000529 Homo sapiens melanocortin 2 receptor (adrenocorticotropic
hormone) M92424 Human homolog of mouse-double-minute 2;
p53-associated mdm2 protein AF007111 MDM2-like p53-binding protein
(MDMX) NM_002415 Homo sapiens macrophage migration inhibitory
factor (glycosylation-inhibiting factor) (MIF), X72755 H. sapiens
Humig mRNA AB014888 Homo sapiens mRNA for MRJ X70040 H. sapiens RON
mRNA for tyrosine kinase; Macrophage stimulating 1 receptor
(c-met-related tyrosine kinase) M30817 Human interferon-induced
cellular resistance mediator protein (MxA) mRNA M30818 Human
interferon-induced cellular resistance mediator protein (MxB) mRNA
U70451 Human myleoid differentiation primary response protein MyD88
mRNA, complete cds NM_000261 Homo sapiens myocilin, trabecular
meshwork inducible glucocorticoid response (MYOC) AF058696 Nijmegen
breakage syndrome 1 (nibrin) U08015 Human NF-ATc mRNA, complete cds
U43341 Human transcription factor NFAT1 isoform B (NFAT1) mRNA,
complete cds L41067 Homo sapiens NF-AT4c mRNA, complete cds L41066
Homo sapiens NF-AT3 mRNA, complete cds U26173 Human bZIP protein
NF-IL3A (IL3BP1) mRNA, complete cds M58603 Human nuclear factor
kappa-B DNA binding subunit (NF- kappa-B) mRNA, p105 X61498 H.
sapiens mRNA for NF-kB subunit (p49/p100) M69043 Homo sapiens MAD-3
mRNA encoding IkB-like activity, complete cds, IkBalpha L40407 Homo
sapiens thyroid receptor interactor (TRIP9) gene, complete cds
[0140]
25TABLE 25 U91616 Human I kappa B epsilon (IkBe) mRNA, complete cds
X77909 H. sapiens IKBL mRNA U16258 Human I kappa BR mRNA, complete
cds U08191 Human R kappa B mRNA, complete cds X52599 Human mRNA for
beta nerve growth factor M14764 Human nerve growth factor receptor
mRNA D50420 Non-histone chromosome protein 2 (S. cerevisiae)-like 1
U17327 Human neuronal nitric oxide synthase (NOS1) mRNA U20141
Human inducible nitric oxide synthase mRNA M93718 Human nitric
oxide synthase mRNA (endothelial) M10901 Human glucocorticoid
receptor alpha mRNA, complete cds L12260 Human recombinant glial
growth factor 2 mRNA, complete cds and flanking regions (neuregulin
1) M86528 Human neurotrophin-4 (NT-4) gene; neurotrophin 5
(neurotrophin 4/5) (NTF5) U46752 Oxidative stress induced like;
Human phosphotyrosine independent ligand p62B B-cell isoform for
the Lck SH2 domain mRNA, partial cds M25650 Human oxytocin mRNA
X64878 H. sapiens mRNA for oxytocin receptor AF000546 Homo sapiens
purinergic receptor P2Y5 mRNA U24152 Human p21-activated protein
kinase (PAK-alpha; PAK1) U24153 Human p21-activated protein kinase
(PAK-gamma; PAK2); PAK65; S6/H4 kinase U41745 Human PDGF associated
protein mRNA (PAP) NM_002592 Homo sapiens proliferating cell
nuclear antigen (PCNA) mRNA AF100928 Homo sapiens
apoptosis-inducing factor AIF mRNA, nuclear gene encoding
mitochondrial protein; Programmed cell death 8 X06374 Human
platelet-derived growth factor A subunit precursor (PDGFA; PDGF-1)
M21574 Human platelet-derived growth factor receptor alpha (PDGFRA)
mRNA; CD140A antigen
[0141]
26TABLE 26 M21616 Human platelet-derived growth factor receptor
mRNA (PDGFRB); CD140B antigen M28526 Platelet/endothelial cell
adhesion molecule (CD31 antigen), neutrophil; CD31 NM_006211 Homo
sapiens proenkephalin (PENK), mRNA X54936 H. sapiens mRNA for
placenta growth factor (P1GF). AF010310 p53 induced protein
(Proline oxidase homolog) Y13367 H. sapiens mRNA for
phosphoinositide 3-kinase; Phosphoinositide-3-kinase, class 2,
alpha polypeptide Y11312 H. sapiens mRNA for phosphoinositide
3-kinase, Phosphoinositide-3-kinase, class 2, beta polypeptide
AJ000008 Homo sapiens mRNA for C2 domain containing PI3-kinase,
phosphoinositide-3-kinase, class 2, gamma polypeptide Z46973 H.
sapiens mRNA for phosphatidylinositol 3-kinase,
Phosphoinositide-3-kinase, class 3 U79143 Human phosphoinositide
3'-hydroxykinase p110-alpha subunit mRNA, Phosphoinositide-3-kina-
se, catalytic, alpha polypeptide S67334 phosphatidylinositol
3-kinase p110 beta isoform = 110 kda catalytic subunit [human, mRNA
Partial, 3213 nt]. Phosphoinositide-3-kinase, catalytic, beta
polypeptide U86453 Human phosphatidylinositol 3-kinase catalytic
subunit p110delta mRNAPhosphoinositide-3-kinase, catalytic, delta
polypeptide X83368 H. sapiens mRNA for phosphatidylinositol 3
kinase gamma, Phosphoinositide-3-kinase, catalytic, gamma
polypeptide M61906 Human P13-kinase associated p85,
Phosphoinositide-3- kinase, regulatory subunit, polypeptide 1 (p85
alpha) X80907 H. sapiens mRNA for p85 beta subunit of phosphatidyl-
inositol-3-kinase, Phosphoinositide-3-kinase, regulatory subunit,
polypeptide 2 (p85 beta) D88532 Homo sapiens mRNA for p55pik,
Phosphoinositide-3-kinase, regulatory subunit, polypeptide 3 (p55,
gamma) Y08991 H. sapiens mRNA for adaptor protein p150,
Phosphoinositide-3-kinase, regulatory subunit 4 M72393 Human
calcium-dependent phospholipid-binding protein (PLA2) mRNA;
Phospholipase A2, group IVA (cytosolic) NM_003560 Homo sapiens
phospholipase A2, group VI (cytosolic, calcium-independent)
(PLA2G6) AF019770 Homo sapiens macrophage inhibitory cytokine-1
(MIC-1) mRNA (prostate differentiation factor)
[0142]
27TABLE 27 M95678 Homo sapiens phospholipase C-beta-2 mRNA;
Phospholipase C, beta 2 Z16411 H. sapiens mRNA encoding
phospholipase c; Phospholipase C, beta 3
(phosphatidylinositol-specific) L41349 Homo sapiens phospholipase C
beta 4 (PLCB4) mRNA; Phospholipase C, beta 4 M34667 Human
phospholipase C-gamma mRNA, complete cds X05199 Human mRNA for
plasminogen J03727 Human phenylethanolamine N-methyltransferase
mRNA, complete cds NM_000939 Homo sapiens proopiomelanocortin
(adrenocorticotropin/ beta-lipotropin/ alpha-melanocyte stimulating
hormone/ beta-melanocyte stimulating hormone/ beta-endorphin)
(POMC) NM_000306 Homo sapiens POU domain, class 1, transcription
factor 1 (Pit1, growth hormone factor 1) (POU1F1) L14778 Human
calmodulin-dependent protein phosphatase catalytic subunit (PPP3CA)
mRNA, complete cds and alternative exon M29551 Human calcineurin A2
mRNA; S46622 calcineurin A catalytic subunit [human, testis, mRNA,
2134 nt]; Protein phosphatase 3 (formerly 2B), catalytic subunit,
gamma isoform (calcineurin A gamma) M28393 Human perforin mRNA,
complete cds X52479 Human PKC alpha mRNA for protein kinase C
alpha; Protein kinase C, alpha AL049654 Novel human mRNA similar to
mouse gene PICK1; Protein kinase C, alpha binding protein X06318
Human mRNA for protein kinase C (PKC) type beta I.; Protein kinase
C, beta 1 U48251 Homo sapiens protein kinase C-binding protein
RACK7 mRNA, partial cds; Protein kinase C binding protein 1 U48250
Human protein kinase C-binding protein RACK17 mRNA, partial cds;
Protein kinase C binding protein 2 D10495 Homo sapiens mRNA for
protein kinase C delta-type; Protein kinase C, delta X65293 H.
sapiens mRNA for protein kinase C-Epsilon; Protein kinase C,
epsilon Z15114 H. sapiens mRNA for protein kinase C gamma
(partial); Protein kinase C, gamma M55284 Human protein kinase C-L
(PRKCL) mRNA; Protein kinase C, eta L18964 Human protein kinase C
iota isoform (PRKCI) mRNA; Protein kinase C, iota D26181 Human mRNA
for novel protein kinase PKN; Protein kinase C-like 1 U33052 Human
lipid-activated, protein kinase PRK2 mRNA; Protein kinase C-like 2
X75756 H. sapiens mRNA for protein kinase C mu; Protein kinase C,
mu AB015982 Homo sapiens EPK2 mRNA for serine/threonine kinase;
Protein kinase C, nu
[0143]
28TABLE 28 L07032 Human protein kinase C theta (PKC) mRNA; Protein
kinase C, theta J03075 Human 80K-H protein (kinase C substrate)
mRNA; Protein kinase C substrate 80K-H Z15108 H. sapiens mRNA for
protein kinase C zeta; Protein kinase C, zeta U47077 Homo sapiens
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) mRNA
[0144]
29TABLE 29 M59979 prostaglandin G/H synthase 1 precursor (PGH
synthase 1; PGHS1; PTGS1); cyclooxygenase 1 (COX1) M90100
prostaglandin G/H synthase 2 precursor (PGH synthase 2; PGHS2;
PTGS2); cyclooxygenase 2 (COX2) D13540 Homo sapiens SH-PTP3 mRNA
for protein-tyrosine phosphatase; Protein tyrosine phosphatase,
non-receptor type 11; Shp2 D21210 Human mRNA for protein tyrosine
phosphatase (PTP-BAS, type 2); Protein tyrosine phosphatase,
non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase); FAP
X62055 H. sapiens PTP1C mRNA for protein-tyrosine phosphatase 1C.;
Protein tyrosine phosphatase, non-receptor type 6; SHP-1 D11327
Human mRNA for protein-tyrosine phosphatase; Protein tyrosine
phosphatase, non-receptor type 7, HePTP Y00062 Human mRNA for T200
leukocyte common antigen (CD45, LC-A). AF060231 Homo sapiens
herpesvirus entry protein C (HVEC) mRNA; Poliovirus
receptor-related 1 (herpesvirus entry mediator C; nectin) M29870
Human ras-related C3 botulinum toxin substrate (rac) mRNA
ras-related C3 botulinum toxin substrate 1; p21-rac1; ras-like
protein TC25 M29871 Human ras-related C3 botulinum toxin substrate
(rac) mRNA; p21-rac2; small G protein Z75311 RAD50 (S. cerevisiae)
homolog AF029670 RAD51 (S. cerevisiae) homolog C AF086904 Protein
kinase Chk2 M23379 Human GTPase-activating protein ras p21 (RASA)
mRNA; GAP M15400 Human retinoblastoma susceptibility mRNA, complete
cds (RB1) NM_002892 Homo sapiens retinoblastoma-binding protein 1
(RBBP1) mRNA S66431 RBP2 = retinoblastoma binding protein 2 [human,
Nalm-6 pre-B cell leukemia, mRNA, 6455 nt]. X74262 Human chromatin
assembly factor 1 p48 subunit (CAF1 p48 subunit);
retinoblastoma-binding protein 4 X85134 H. sapiens RBQ-3 mRNA
X85133 H. sapiens RBQ-1 mRNA U35143 Human retinoblastoma-binding
protein (RbAp46) mRNA, complete cds AF043431 Homo sapiens
retinoblastoma-interacting protein (RBBP8) mRNA, complete cds
[0145]
30TABLE 30 AF039564 Homo sapiens retinoblastoma binding protein
(RBBP9) mRNA, complete cds. L14812 Human retinoblastoma related
protein (p107) mRNA; Retinoblastoma-like 1 X74594 Human
retinoblastoma-like protein 2 (RBL2; RB2); 130-kDa
retinoblastoma-associated protein (p130) L19067 Human NF-kappa-B
transcription factor p65 subunit mRNA, complete cds. M83221 Homo
sapiens I-Rel mRNA, complete cds. NM_000537 Homo sapiens renin
(REN) AF037195 Homo sapiens regulator of G protein signaling RGS14
mRNA, complete cds. U50062 Homo sapiens RIP protein kinase mRNA,
Receptor (TNFRSF)-interacting serine-threonine kinase 1 AF027706
Homo sapiens serine/threonine kinase RICK (RICK) mRNA; RIP2 M63488
Replication protein A1 (70 kD) X56932 H. sapiens mRNA for 23 kD
highly basic protein U14971 Human ribosomal protein S9 mRNA,
complete cds AF020044 Homo sapiens lymphocyte secreted C-type
lectin precursor, mRNA, complete cds M57502 Human secreted protein
(I-309) mRNA; Small inducible cytokine A1 (I-309, homologous to
mouse Tca-3) D49372 Human mRNA for eotaxin; Small inducible
cytokine subfamily A (Cys-Cys), member 11 (eotaxin) U59808 Human
monocyte chemotactic protein-4 precursor (MCP-4) mRNA; Small
inducible cytokine subfamily A (Cys-Cys), member 13 Z49270 H.
sapiens mRNA for chemokine HCC-1; Small inducible cytokine
subfamily A (Cys-Cys), member 14 AF031587 Homo sapiens MIP-1 delta
mRNA; Small inducible cytokine subfamily A (Cys-Cys), member 15
AF039955 Homo sapiens liver CC chemokine-1 precursor (SCYA16) mRNA;
Small inducible cytokine subfamily A, member 16 D43767 Human mRNA
for chemokine; Small inducible cytokine subfamily A (Cys-Cys),
member 17 Y13710 Homo sapiens mRNA for alternative activated
macrophage specific CC chemokine 1; Small inducible cytokine
subfamily A (Cys-Cys), member 18, pulmonary and
activation-regulated U77180 Human macrophage inflammatory protein 3
beta (MIP-3beta), Small inducible cytokine subfamily A (Cys-Cys),
member 19 S71513 monocyte chemoattractant protein-1 [human, mRNA,
739 nt], MCP-1
[0146]
31TABLE 31 U77035 Human macrophage inflammatory protein 3 alpha
(MIP-3a) mRNA; Small inducible cytokine subfamily A (Cys-Cys),
member 20 AF001979 Homo sapiens beta chemokine mRNA; Small
inducible cytokine subfamily A (Cys-Cys), member 21 U83171 Human
macrophage-derived chemokine precursor (MDC) mRNA; Small inducible
cytokine subfamily A (Cys-Cys), member 22 U58913 Human chemokine
(hmrp-2a) mRNA; small inducible cytokine subfamily A (Cys-Cys),
member 23 U85768 Human myeloid progenitor inhibitory factor-1
MPIF-2 mRNA
[0147]
32TABLE 32 U86358 Human chemokine (TECK) mRNA; Small inducible
cytokine subfamily A (Cys-Cys), member 25 AB010447 Homo sapiens
mRNA for CC chemokine eotaxin3;Small inducible cytokine subfamily A
(Cys-Cys), member 26 AJ243542 Homo sapiens maRNA for CCL27
chemokine, small inducible cytokine subfamily A (Cys-Cys), member
27 M23452 Human macrophage inflammatory protein (G0S19-1) mPNA,
Small inducible cytokine subfamily A (Cys-Cys), member 3; Mip-1a
J04130 Human activation (Act-2) mRNA, complete cds M21121 Human T
cell-specific protein (RANTES) mRNA, Small inducible cytokine A5
X72308 Homo sapiens mRNA for monocyte chemotactic protein-3
(MCP-3), Small inducible cytokine A7 (monocyte chemotactic protein
3) Y10802 H. sapiens mRNA for monocyte chemotactic protein 2 X02530
Human mRNA for gamma-interferon inducible early response gene (with
homology to platelet proteins). AF030514 Homo sapiens interferon
stimulated T-cell alpha chemoattractant precursor, mRNA, complete
cds AF073957 Homo sapiens CXC chemokine BRAK mRNA,Small inducible
cytokine subfamily B (Cys-X-Cys), member 14 X78686 H. sapiens
ENA-78 mRNA; Small inducible cytokine subfamily B (Cys-X-Cys),
member 5 (epithelial-derived neutrophil-activating peptide 78)
U81234 Human chemokine alpha 3 (CKA-3) mRNA; small inducible
cytokine subfamily B (Cys-X-Cys), member 6 (granulocyte chemotactic
protein 2) D43768 numan mPNA for SCM-1 (single cysteine motif-1);
Small inducible cytokine subfamily C, member 1 (lymphotactin)
NM_003175 Homo sapiens small inducible cytokine subfamily C, member
2 (SCYC2), mRNA. U84487 Human CX3C chemokine precursor, mFNA,
alternatively spliced, complete cds U10117 Human
endothelial-monocyte activating polypeptide II mPNA; small
inducible cytokine subfamily E, member 1 (endothelial
monocyte-activating) L36033 Human pre-B cell stimulating factor
homologue (SDF1b) mRNA, complete cds; Stromal cell-derived factor 1
M30640 selectin E (endothelial adhesion molecule 1) M25280 selectin
L (lymphocyte adhesion molecule 1)
[0148]
33TABLE 33 M25322 selectin P (granule membrane protein 140 kD,
antigen CD62) U02297 selectin P ligand X68148 H. sapiens SHC mFNA,
Src homology 2 domain-containing transforming protein 1 M20747
Human insulin-responsive glucose transporter (GLUT4) mPNA; Solute
carrier family 2 (facilitated glucose transporter), member 4
NM_001043 Homo sapiens solute carrier family 6 (neurotransmitter
transporter, noradrenalin), member 2 (SLC6A2) NM_000454 Homo
sapiens superoxide dismutase 1, soluble (amyotrophic lateral
sclerosis 1 (adult)) (SOD1); Superoxide dismutase 1, soluble
(amyotrophic lateral sclerosis 1 (adult)) X07834 Human mRNA for
manganese superoxide dismutase; Superoxide dismutase 2,
mitochondrial J02947 Human extracellular-superoxide dismutase
(SOD3) mRNA; Superoxide dismutase 3, extracellular L13858 Human
guanine nucleotide exchange factor mRNA, complete cds, SOS1, Sons
of Sevenless M60618 Human nuclear autoantigen (SP-100) mRNA
NM_000582 Homo sapiens secreted phosphoprotein 1 (osteopontin, bone
sialoprotein I, early T-lymphocyte activation 1) (SPP1) U83867
Human alpha II spectrin mPNA, Fodrin J03161 Human serum response
factor (SRF) mRNA; Serum response factor (c-fos serum response
element-binding transcription factor) D86640 Homo sapiens mRNA for
stac, (src homology three (SH3) and cysteine rich domain) M97935
Homo sapiens transcription factor ISGF-3 mRNA, complete cds M97934
Homo sapiens interferon alpha induced transcriptional activator
(ISGF-3) mRNA sequence L29277 Homo sapiens DNA-binding protein
(APRF) mRNA, complete cds L78440 Homo sapiens STAT4 mRNA, complete
cds L41142 Homo sapiens signal transducer and activator of
transcription (STATS) mPNA U16031 Human transcription factor IL-4
Stat mPNA, complete cds U04735 Human microsomal stress 70 protein
ATPase core (stch) mRNA; Stress 70 protein chaperone,
microsome-associated, 60 kD U26424 Human Ste20-like kinase (MST2)
mRNA; Serine/threonine kinase 3 (Ste20, yeast homolog) U60207 Human
stress responsive serine/threonine protein kinase Krs-2 mRNA,
Serine/threonine kinase 4
[0149]
34TABLE 34 L28824 Homo sapiens protein tyrosine kinase (Syk) mPNA;
Spleen tyrosine kinase U49928 Homo sapiens TAK1 binding protein
(TAB1) mRNA, complete cds U63830 Human TRAF family
member-associated NF-kB activator TANK mPNA, 1-TRAF M57732 Human
hepatic nuclear factor 1 (TCF1) mPNA M83233 Homo sapiens
transcription factor (HTF4) mPNA, complete cds U08336 Human basic
helix-loop-helix transcription factor mRNA, complete cds D89928
Homo sapiens HKL1 mRNA, complete cds
[0150]
35TABLE 35 NM_007109 Homo sapiens transcription factor 19 (SC1)
(TCF19), mRNA X58840 Human mRNA for variant hepatic nuclear factor
1 (vHNF1), TCF2 U19345 Homo sapiens AR1 (TCF20) mRNA, partial cds
AF047419 Homo sapiens epicardin mRNA, complete cds. M31523 Human
transcription factor (E2A) mRNA, complete cds NM_003199 Homo
sapiens transcription factor 4 (TCF4) M62810 Human mitochondrial
transcription factor 1 mRNA NM_003202 Homo sapiens transcription
factor 7 (T-cell specific, HMG-box) (TCF7) mRNA. Y11306 Homo
sapiens mRNA for hTCF-4 D15050 Human mRNA for transcription factor
AREB6; Transcription factor 8 (represses interleukin 2 expression)
D43642 Human YL-1 mRNA for YL-1 protein (nuclear protein with
DNA-binding ability), complete cds AB012124 Homo sapiens TCFL5 mRNA
for transcription factor-like 5, complete cds NM_003212 Homo
sapiens teratocarcinoma-derived growth factor 1 (TDGF1) mRNA L23959
Homo sapiens E2F-related transcription factor (DP-1) mRNA, complete
cds. NM_003227 Homo sapiens transferrin receptor 2 (TFR2), mRNA
X01060 Human mRNA for transferrin receptor X70340 H. sapiens mRNA
for transforming growth factor alpha X02812 Human transforming
growth factor-beta (TGF-beta; TGFB) M19154 Human transforming
growth factor-beta-2 mRNA; M19154 glioblastoma-derived T-cell
suppressor factor (G-TSF); bsc-1 cell growth inhibitor; polyergin;
cetermin J03241 Human transforming growth factor-beta 3 (TGF-beta3)
mRNA, complete cds. L11695 Human activin receptor-like kinase
(ALK-5) mRNA, complete cds D50683 Homo sapiens mRNA for TGF-betaIIR
alpha, complete cds L07594 Human transforming growth factor-beta
type III receptor (TGF-beta) mRNA, complete cds NM_000360 Homo
sapiens tyrosine hydroxylase (TH), mRNA L33410 Human c-mpl ligand
(ML) mRNA, complete cds NM_006288 Homo sapiens Thy-1 cell surface
antigen (THY1), mRNA U02571 Human tissue inhibitor of
metalloproteinase-3 precursor (TIMP-3) mRNA, complete cds
[0151]
36TABLE 36 U88540 Homo sapiens Toll-like receptor 1 (TLR1) mRNA,
complete cds U88878 Homo sapiens Toll-like receptor 2 (TLR2) mRNA,
complete cds U88879 Homo sapiens Toll-like receptor 3 (TLR3) mRNA,
complete cds U88880 Homo sapiens Toll-like receptor 4 (TLR4) mRNA,
complete cds U88881 Homo sapiens Toll-like receptor 5 (TLR5) mRNA,
partial cds. M10988 Human tumor necrosis factor (TNF) mRNA M59465
Human tumor necrosis factor alpha inducible protein A20 mRNA
complete cds M31165 Tumor necrosis factor, alpha-induced protein 6
AF016268 Homo sapiens death receptor 5 (DR5) mRNA, Tumor necrosis
factor receptor superfamily, member 10b AF016267 Homo sapiens TRAIL
receptor 3 mRNA, complete cds AF018253 Homo sapiens receptor
activator of nuclear factor-kappa B (RANK) mRNA, complete cds
U94332 Human osteoprotegerin (OPG) mRNA, complete cds U74611 Human
Apo-3 mRNA; Tumor necrosis factor receptor superfamily, member 12
(translocating chain-association membrane protein) NM_001192 Homo
sapiens tumor necrosis factor receptor superfamily, member 17
(TNFRSF17), mRNA X55313 H. sapiens TNF-R mRNA for tumor necrosis
factor receptor type 1. M32315 Human tumor necrosis factor receptor
mRNA, TNF R2 X75962 H. sapiens mRNA for OX40 homologue X60592 Human
CDw40 mRNA for nerve growth factor receptor- related B-lymphocyte
activation molecule; CD40 X63717 H. sapiens mRNA for APO-1 cell
surface antigen, FAS M83554 H. sapiens lymphocyte activation
antigen CD30 mRNA, complete cds L12964 Human activation dependent T
cell mRNA, complete cds U37518 Human TNF-related apoptosis inducing
ligand TRAIL mRNA, complete cds AF053712 Homo sapiens
osteoprotegerin ligand mRNA, complete cds
[0152]
37TABLE 37 AF039390 Homo sapiens vascular endothelial cell growth
inhibitor (VEGI) mRNA, partial cds D90224 Human mRNA for
glycoprotein 34 (gp34) L07414 Human CD40-ligand mRNA (Tumor
necrosis factor (ligand) superfamily, member 5); CD40L D38122 Human
mRNA for Fas ligand, complete cds; FasL L09753 Homo sapiens CD30
ligand mRNA, complete cds. U03398 Human receptor 4-1BB ligand mRNA,
complete cds M14695 Human p53 cellular tumor antigen mRNA, complete
cds U58334 Human Bc12, p53 birLding protein Bbp/53BP2 (BBP/53BP2)
mRNA NM_005427 Homo sapiens tumor protein p73 (TP73) mPNA: Human
p73 (monoallelically expressed p53-related protein) X02592 Human
mRNA for T-cell receptor alpha chain (TCR-alpha). L41690 Homo
sapiens TNF receptor-1 associated protein (TRADD) mRNA, 3' end of
cds NM_005658 Homo sapiens TNF receptor-associated factor 1 (TRAF1)
mRNA. U12597 Human tumor necrosis factor type 2 receptor associated
protein (TRAP3) mRNA, complete cds NM_003300 Homo sapiens TNF
receptor-associated factor 3 (TPAF3) mRNA. X80200 H. sapiens MLN62
mRNA (TNF receptor-associated factor 4) AB000509 Homo sapiens mRNA
for TRAF5, complete cds U78798 Human TNF receptor associated factor
6 (TRAF6) mRNA, complete cds AF043254 Homo sapiens heat shock
protein 75 (hsp75) mRNA, partial cds (tumor necrosis factor type 1
receptor associated protein ) M12886 Human T-cell receptor active
beta-chain mRNA, complete cds U35048 Human putative regulatory
protein TGF-beta-stimulated clone 22 homolog (TSC22) NM_000549 Homo
sapiens thyroid stimulating hormone, beta (TSHB) NM_000369 Homo
sapiens thyroid stimulating hormone receptor (TSHR) X54637 Human
tyk2 mRNA for non-receptor protein tyrosine kinase; Tyrosine kinase
2 M26880 Human ubiquitin mRNA, complete cds AF016371 Homo sapiens
U-snRNP-associated cyclophilin (USA-CyP) mRNA, complete cds
NM_001078 Homo sapiens vascular cell adhesion molecule 1 (VCAM1)
M32977 Human heparin-binding vascular endothelial growth factor
(VEGF) mRNA U48801 Human vascular endothelial growth factor B
precursor (VEGFB)
[0153]
38TABLE 38 U43142 Human vascular endothelial growth factor related
protein VRP mRNA vascular endothelial growth factor C precursor
(VEGF-C); FLT4 ligand U10564 Human CDK tyrosine 15-kinase WEE1Hu
(Wee1Hu) mRNA, complete cds. AF100779 Homo sapiens connective
tissue growth factor related protein WISP-1 (WISP1) mRNA, complete
cds AF100780 Homo sapiens connective tissue growth factor related
protein WISP-2 (WISP2) mRNA, complete cds. AF100781 Homo sapiens
connective tissue growth factor related protein WISP-3 (WISP3)
mRNA, complete cds. U81787 Human Wnt10B mRNA, complete cds Y12692
Homo sapiens mRNA for WNT11 gene X07876 Human mRNA for irp protein
(int-1 related protein) Wingless-type MMTV integration site family
member 2 Z71621 H. sapiens Wnt-13 mRNA U53476 Human proto-oncogene
Wnt7a mRNA, complete cds. Y11094 H. sapiens mRNA for WNT-8B protein
L20422 Human 14-3-3n protein mRNA; Tyrosine 3-
monooxygenase/tryptophan 5-monooxygenase activation protein, eta
polypeptide M86400 Human phospholipase A2 mRNA, complete cds L05148
Human protein tyrosine kinase related mRNA sequence; Zeta-chain
(TCR) associated protein kinase (70 kD)
[0154]
39TABLE 39 1 CD3 - cell/CD3 + cell Name ave (n = 3) stdev CV (%)
ABCC3 21.92 8.05 36.73 LYN 14.90 0.09 40.15 PTGS1 14.66 8.94 0.58
CDKN1C 14.00 11.98 85.57 FLT3 13.91 7.16 51.49 FCER1G 13.20 12.96
91.63 CHUK 11.63 3.76 32.30 VEGFC 10.80 4.31 39.92 POLK 10.65 10.14
95.21 AVPR1A 10.22 6.37 62.29 CYP7A1 9.66 2.67 27.70 PRKCBP2 9.62
9.49 98.70 GNG11 8.14 4.24 52.03 GNAZ 8.06 2.92 36.17 AVPR2 7.72
5.35 69.27 CD9 7.62 1.50 19.69 GJB3 7.49 4.21 79.72 DTR 7.39 2.97
40.21 HLA-DRB1 7.31 4.82 81.16 RPC32 7.30 5.82 79.79 NRG1 7.25 2.92
61.00 MAFG 7.19 3.82 29.64 MGST2 6.95 3.36 48.37 RAB13 6.75 2.38
22.94 SLC7A7 6.38 1.63 25.63 CYP1B1 6.36 3.18 50.01 IL6 6.07 2.06
33.91 PDGFA 6.07 2.96 48.81 MYCL1 6.06 3.14 30.99 FES 6.04 4.23
70.04 TNFRSF1B 5.86 3.74 63.82 IPF1 5.79 5.75 99.45 YWHAH 5.46 1.61
29.41 PIG3 5.31 2.78 67.68 BTK 5.26 2.92 55.53 E2F3 5.00 2.52 50.53
FCGR2B 4.92 1.53 44.29 UGT2B7 4.72 2.70 40.31 ATP1B4 4.66 3.77
81.02 PENK 4.63 0.82 17.65 BAG4 4.60 1.53 85.30 PLA2G4A 4.48 2.87
64.04 TLR4 4.46 0.89 19.95 FGR 4.32 0.93 33.34 ALDH1 4.22 2.58
61.08 NOS1 4.21 2.74 65.02 TLR5 4.14 1.23 51.76 ABCC1 4.09 2.77
78.31 ALDH2 4.08 3.04 65.86 ARHGAP6 4.08 0.86 21.04 IL1R2 3.88 1.88
57.22 SOD2 3.76 0.66 17.57 NR1H4 3.66 1.59 43.29 TCF4 3.65 0.90
95.71 SKIL 3.42 0.71 20.79 IL8RA 3.41 0.72 74.47 POU2F2 3.36 0.77
49.91 CDC25C 3.33 1.34 42.41 PAK1 3.28 1.25 37.96 SLC1A4 3.19 0.69
21.61 SLC1A3 3.15 0.72 22.93 BRAF 3.13 0.07 2.37 ATF3 3.11 0.46
14.66
[0155]
40TABLE 39 2 CD3 - cell/CD3 + cell Name ave (n = 3) stdev CV (%)
TRA@ 15.08 11.13 73.78 CD3G 12.03 1.36 11.32 CD3E 10.55 1.10 10.39
IL7R 9.77 6.15 62.90 BCL2 9.54 2.88 30.18 PCNA 8.14 4.35 53.41
HSPA10 7.52 3.62 48.14 EPHX2 7.04 2.33 33.07 CD8B1 6.97 3.98 57.03
FYN 6.97 0.97 13.87 STAT1 6.44 3.54 54.87 HSPF1 6.44 0.87 13.55
CCR5 5.63 2.43 43.20 ELF1 5.33 3.42 64.21 NR3C2 5.22 4.78 91.53
TGFBR2 5.01 2.88 57.45 ATRX 4.65 2.49 53.64 HLJ1 4.64 3.41 73.62
CYP2J2 4.58 1.29 28.22 E2F4 4.44 1.96 44.28 STAT4 4.35 4.75 108.99
NFATC3 4.26 2.62 61.62 PIK3R1 4.17 1.23 29.47 PPP3CB 4.12 2.00
48.48 CLK1 4.11 4.04 98.37 RBL2 3.76 2.16 57.55 KIAA0194 3.75 0.91
24.32 GSTM3 3.75 2.21 58.89 GZMA 3.74 4.32 115.44 CDC25B 3.70 0.50
13.54 KRAS2 3.65 0.98 26.90 ITGA4 3.49 1.62 46.24 IL13RA2 3.48 2.01
57.64 SOD1 3.47 0.21 6.20 CCNG1 3.38 1.25 36.86 PAP 3.30 0.87 26.40
ABCE1 3.27 0.48 14.75 TNFRSF1 3.25 1.01 30.96 CHST5 3.19 2.34 73.37
STAC 3.16 2.62 82.98 ATP1A3 3.14 0.87 27.84 HINT 3.14 1.49 47.46
ABCC5 3.12 1.06 34.01 TAF1B 3.11 1.33 42.84 CD80 3.10 0.20 6.29
CD28 3.10 0.94 30.25 STCH 3.08 0.86 27.91 TTF1 3.07 0.73 23.81
POLR2C 3.05 1.49 48.89 HGF 3.01 1.37 45.36
[0156]
41 TABLE 40 Name of gene t value p value ABCE1 -24.009 0.000071
IFNB1 -16.646 0.000299 BMI1 -15.039 0.000443 KRAS2 -14.382 0.000527
CD80 -14.224 0.000550 IL8RA 13.916 0.000598 BAG4 13.105 0.000754
POLK 13.054 0.000766 NFATC2 -12.400 0.000933 NRG1 12.049 0.001041
TLR5 11.925 0.001083 HGF -10.946 0.001501 POLI -10.621 0.001682
CDC25B -10.463 0.001780 IL6 10.452 0.001787 SELE -10.449 0.001789
MAX 10.384 0.001832 FCGR2B 10.296 0.001891 COX10 -10.208 0.001953
YWHAH 10.138 0.002005 ADH6 9.976 0.002130 PRKCZ -9.925 0.002171
AVPR2 9.872 0.002215 GJB3 9.808 0.002269 CLK2 -9.694 0.002371 TRA@
-9.543 0.002514 EPHX2 -9.540 0.002517 CD3G -9.441 0.002617 MAP2K6
-9.413 0.002646 ALDH1 9.196 0.002886 PCNA -9.134 0.002959 CD3E
-9.131 0.002962
* * * * *
References