Module 15

General Properties
Below we list the number of gene sets from which the module was composed was originally composed, and the number of genes and experiments that it contains. Clicking on the number of genes will display a detailed list of all the genes in the module. Clicking on the number of experiments will display a detailed list of all the experiments in the module.
Num gene sets:	2
Num genes:	359 (see 2510 additional genes for this module)
Num experiments:	869 (254 induced, 615 repressed)
Parent module:	53
Children modules:	None

Gene sets
Below we list the gene sets from which the module was originally composed. Clicking on a gene set will display all the genes associated with that gene set. Also listed are all the other modules in which the gene set participates.
THY__2
THY__1

Enriched clinical annotations
For each of the clinical annotations, we tested whether it was enriched in the set of arrays in which the module is significantly induced (or repressed). Below we list all such annotations that were enriched in this module with an FDR corrected p-value of 0.05 ('P-value' column), along with the number ('Hits' column) of induced (or repressed) module's arrays in which they appear. We also show the fraction of the module's induced (or repressed) arrays with the given annotation ('Hits (%)' column). For completeness, we also list the total number of relevant induced arrays in the module ('Module hits in category' column), total number of arrays in the compendium in which the corresponding annotation is present ('Arrays in annotation' column), and the total number of relevant arrays in the compendium ('Arrays' column). Note that the 'relevant' arrays may be different for each annotation, since it includes only arrays in which the annotation was relevant (i.e., present or not present) and excludes arrays where the value of the annotation was not known. Rows that correspond to annotations that were enriched in the induced arrays of the module have a red background, while rows corresponding to annotations enriched in the repressed arrays have a green background. For each annotation, we also list the other modules in which it was enriched.
Clinical annotation	Category	P-value	Hits	Hits(%)	Module hits in category	Arrays in annotation	Arrays
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	2.9e-21	28	70	40	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	2.9e-21	28	70	40	30	182
Prostate (Prostate cancer*)	Prostate cancer*	7.5e-18	73	11.8	615	101	1945
Cancer and cell line (Various tumors*)	Various tumors*	1.3e-15	72	11.7	615	105	1945
Cancer (Various tumors*)	Various tumors*	1.3e-15	72	11.7	615	105	1945
Epithelial cell line (NCI60)	NCI60	1.5e-12	32	46.3	69	32	139
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	8.0e-10	25	9.8	254	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	8.0e-10	25	9.8	254	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	8.0e-10	25	9.8	254	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	8.0e-10	25	9.8	254	53	1945
Liver tissue (Liver cancer*)	Liver cancer*	2.9e-08	51	20.0	254	187	1945
CNS tissue, cancer or cell line (Neuro tumors*)	Neuro tumors*	3.2e-08	51	8.2	615	85	1945
Hematologic cancer and cell line (NCI60)	NCI60	8.1e-08	9	64.2	14	14	139
Hematologic samples and cell lines (NCI60)	NCI60	8.1e-08	9	64.2	14	14	139
Leukemia cell line (NCI60)	NCI60	8.1e-08	9	64.2	14	14	139
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.9e-07	51	20.0	254	197	1945
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	4.8e-07	47	7.6	615	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	4.8e-07	47	7.6	615	81	1945
Female hormonal cancer cell line (Breast cancer)	Breast cancer	9.4e-07	9	52.9	17	15	152
Breast cancer cell line (Breast cancer)	Breast cancer	4.1e-06	9	52.9	17	17	152
Cell line (NCI60*)	NCI60*	4.7e-06	67	10.8	615	135	1945
Cancer and cell line (Neuro tumors*)	Neuro tumors*	5.1e-06	47	7.6	615	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	5.1e-06	47	7.6	615	86	1945
Cancer and cell line (NCI60*)	NCI60*	5.5e-06	68	11.0	615	138	1945
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	6.8e-06	26	81.2	32	67	144
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	1.2e-05	22	40.7	54	46	245
Leukemia (B lymphoma)	B lymphoma	1.2e-05	22	40.7	54	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	1.2e-05	22	40.7	54	46	245
Cancer and cell line (Gliomas*)	Gliomas*	1.6e-05	29	4.7	615	47	1945
Cancer (Gliomas*)	Gliomas*	1.6e-05	29	4.7	615	47	1945
CNS cancer or cell line (Gliomas*)	Gliomas*	1.6e-05	29	4.7	615	47	1945
CNS tissue, cancer or cell line (Gliomas*)	Gliomas*	1.6e-05	29	4.7	615	47	1945
CNS tumor (Gliomas*)	Gliomas*	1.6e-05	29	4.7	615	47	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	4.3e-05	38	14.9	254	156	1945
Lung carcinoid (Lung cancer)	Lung cancer	5.0e-05	15	17.0	88	20	276
Classical malignant glioblastoma (Gliomas)	Gliomas	0.0001	10	100	10	14	27
Non-classic anaplastic oligodendroglioma (Gliomas)	Gliomas	0.0001	13	92.8	14	13	20
Hematologic cancer and cell line (Various tumors)	Various tumors	0.0002	5	100	5	31	154
Hematologic cancer (Various tumors)	Various tumors	0.0002	5	100	5	31	154
Primary blood mononuclear cells (Various tumors)	Various tumors	0.0002	5	100	5	31	154
Non-classic malignant glioblastoma (Gliomas)	Gliomas	0.0002	12	80	15	13	27
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	0.0003	40	15.7	254	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	0.0003	40	15.7	254	182	1945
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0003	26	81.2	32	78	144
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0004	5	15.6	32	5	144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0004	5	15.6	32	5	144

Enriched GO annotations
For each GO annotation, we tested whether it was enriched in the set of genes of the module. Below we list all such annotations that were enriched in this module with an FDR corrected p-value of 0.05 ('P-value' column), along with the number ('Hits' column) of the module's genes in which they appear. We also show the fraction of the module's genes with the given GO annotation that are included in this module ('Hits (%)' column). For completeness, we also list the total number of genes in the module ('Module genes' column), total number of genes in the compendium in which the corresponding annotation is present ('Genes in annotation' column), and the total number of genes in the compendium ('Genes' column).
GO annotation	P-value	Hits	Hits(%)	Module genes	Genes in annotation	Genes
nucleoside monophosphate biosynthesis	1.0e-05	6	2.3	256	11	4566
purine ribonucleoside monophosphate biosynthesis	5.5e-05	5	1.9	256	9	4566
ribonucleoside monophosphate metabolism	0.0001	5	1.9	256	10	4566
ribonucleotide biosynthesis	0.0001	7	2.7	256	22	4566

Visual display

Below is a visual display of the module. Shown are those arrays in which the module's genes significantly change, and the direction of change (induction/repression) in each array is indicated (middle, labeled 'Module changes'; red/green row). The arrays that correspond to the significant clinical attributes are also shown (top; brown rows). The gene sets that compose the module are also shown (left) along with an indication of the membership of the module genes in these gene sets.

You can also view the images within GeneXPress by loading the module gxp file file.

Note: Since there are 869 experiments, this image does not display the individual experiment names, but rather condenses each experiment to a single pixel without displaying its name. You can fully view the image for this module within GeneXPress, by loading any of the four files mentioned in the line above

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