Module 117 -- Signaling

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:	731 (see 3382 additional genes for this module)
Num experiments:	1014 (335 induced, 679 repressed)
Parent module:	None
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.
Nutt03 44
Lessnick02 38

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
Liver tissue (Liver cancer*)	Liver cancer*	8.1e-43	110	32.8	335	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.0e-39	110	32.8	335	197	1945
Acute leukemia (Leukemia*)	Leukemia*	2.2e-37	120	17.6	679	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	2.2e-37	120	17.6	679	141	1945
Cancer (Leukemia*)	Leukemia*	2.2e-37	120	17.6	679	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	2.2e-37	120	17.6	679	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	2.2e-37	120	17.6	679	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	2.2e-37	120	17.6	679	141	1945
Leukemia (Leukemia*)	Leukemia*	2.2e-37	120	17.6	679	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	2.2e-37	120	17.6	679	141	1945
Monocytes (Leukemia*)	Leukemia*	2.2e-37	120	17.6	679	141	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.7e-32	89	26.5	335	156	1945
Cancer and cell line (Liver cancer)	Liver cancer	2.4e-23	87	96.6	90	126	207
Non-tumor liver tissue (Liver cancer)	Liver cancer	2.4e-22	72	65.4	110	76	207
Hematologic samples and cell lines (B lymphoma)	B lymphoma	2.9e-16	78	81.2	96	121	245
Cancer and cell line (Various tumors*)	Various tumors*	4.8e-15	75	11.0	679	105	1945
Cancer (Various tumors*)	Various tumors*	4.8e-15	75	11.0	679	105	1945
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	1.3e-14	19	82.6	23	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	1.3e-14	19	82.6	23	30	182
Breast tissue or cancer (Breast cancer*)	Breast cancer*	1.5e-14	55	16.4	335	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	1.5e-14	55	16.4	335	118	1945
Cancer (Liver cancer)	Liver cancer	5.3e-14	76	84.4	90	115	207
Adenocarcinoma (Breast cancer*)	Breast cancer*	1.0e-13	52	15.5	335	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	1.0e-13	52	15.5	335	112	1945
Cancer (Breast cancer*)	Breast cancer*	1.0e-13	52	15.5	335	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	1.0e-13	52	15.5	335	112	1945
Lymphoma (B lymphoma)	B lymphoma	2.3e-11	54	56.2	96	77	245
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	4.7e-11	52	15.5	335	127	1945
Breast cancer or cell line (Breast cancer*)	Breast cancer*	6.8e-11	52	15.5	335	128	1945
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	1.1e-10	55	16.4	335	141	1945
Breast tissue, cancer or cell line (Breast cancer*)	Breast cancer*	1.6e-10	55	16.4	335	142	1945
Adenocarcinoma (Liver cancer)	Liver cancer	3.7e-09	63	70	90	97	207
Cancer and cell line (Breast cancer*)	Breast cancer*	8.0e-09	52	15.5	335	143	1945
Invasive liver tumor (Liver cancer)	Liver cancer	1.5e-08	32	35.5	90	38	207
Hepatocellular carcinoma (Liver cancer)	Liver cancer	2.1e-08	65	72.2	90	104	207
Activated B like DLBCL (B lymphoma)	B lymphoma	4.2e-08	17	42.5	40	30	245
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	2.2e-07	35	87.5	40	126	245
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	1.9e-06	35	87.5	40	134	245
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	9.0e-06	5	31.2	16	5	144
Cell line (Liver cancer)	Liver cancer	7.2e-05	11	12.2	90	11	207
Normal tissue (Liver cancer)	Liver cancer	9.4e-05	14	12.7	110	14	207
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	9.4e-05	37	92.5	40	167	245
Breast cancer cell line (Breast cancer)	Breast cancer	0.0001	13	25.4	51	17	152
Liver cancer cell line (Liver cancer)	Liver cancer	0.0001	10	11.1	90	10	207
Metastasis (Liver cancer)	Liver cancer	0.0001	10	11.1	90	10	207
Cell line (Breast cancer)	Breast cancer	0.0001	19	37.2	51	30	152
GC B like DLBCL (B lymphoma)	B lymphoma	0.0002	18	45	40	53	245
Breast tissue or cancer (NCI60)	NCI60	0.0004	4	19.0	21	4	139
Female hormonal tissue or cancer (NCI60)	NCI60	0.0004	4	19.0	21	4	139

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
response to biotic stimulus	1.2e-08	118	21.1	558	600	4566
chymotrypsin activity	1.2e-06	19	3.4	558	48	4566
secretion	1.4e-06	55	9.8	558	240	4566
trypsin activity	2.5e-06	19	3.4	558	50	4566
cell-cell signaling	9.7e-06	45	8.0	558	194	4566
immune response	1.0e-05	88	15.7	558	469	4566
integral to plasma membrane	1.5e-05	108	19.3	558	612	4566
receptor binding	1.8e-05	51	9.1	558	235	4566
catabolism	6.9e-05	46	8.2	558	215	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 731 genes, this image does not display the individual gene names, but rather condenses each gene 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.

Note: Since there are 1014 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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