Module 94 -- 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:	374 (see 2604 additional genes for this module)
Num experiments:	719 (100 induced, 619 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.
Armstrong01 13
Bhattacharjee01 19

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
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	3.2e-41	188	30.3	619	276	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	6.4e-36	170	27.4	619	252	1945
Cancer (Lung cancer*)	Lung cancer*	6.4e-36	170	27.4	619	252	1945
Acute leukemia (Leukemia*)	Leukemia*	1.1e-34	113	18.2	619	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	1.1e-34	113	18.2	619	141	1945
Cancer (Leukemia*)	Leukemia*	1.1e-34	113	18.2	619	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	1.1e-34	113	18.2	619	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	1.1e-34	113	18.2	619	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	1.1e-34	113	18.2	619	141	1945
Leukemia (Leukemia*)	Leukemia*	1.1e-34	113	18.2	619	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	1.1e-34	113	18.2	619	141	1945
Monocytes (Leukemia*)	Leukemia*	1.1e-34	113	18.2	619	141	1945
Lung cancer (Lung cancer*)	Lung cancer*	4.8e-34	161	26.0	619	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	4.8e-34	161	26.0	619	238	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	1.8e-31	142	22.9	619	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	1.8e-31	142	22.9	619	205	1945
Lymphoma (B lymphoma)	B lymphoma	3.6e-27	53	88.3	60	77	245
Cancer and cell line (Various tumors*)	Various tumors*	6.4e-21	79	12.7	619	105	1945
Cancer (Various tumors*)	Various tumors*	6.4e-21	79	12.7	619	105	1945
Hematologic samples and cell lines (B lymphoma)	B lymphoma	2.7e-15	55	91.6	60	121	245
Non-tumor liver tissue (Liver cancer)	Liver cancer	4.9e-10	27	87.0	31	76	207
Liver tissue (Liver cancer*)	Liver cancer*	5.6e-10	31	31	100	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	2.2e-09	31	31	100	197	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	4.0e-09	37	37	100	276	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	4.8e-09	35	35	100	252	1945
Cancer (Lung cancer*)	Lung cancer*	4.8e-09	35	35	100	252	1945
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	1.8e-07	56	93.3	60	167	245
Lung cancer (Lung cancer*)	Lung cancer*	8.8e-07	30	30	100	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	8.8e-07	30	30	100	238	1945
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	9.8e-07	47	78.3	60	126	245
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.5e-06	23	23	100	156	1945
Cancer and cell line (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	1.0e-05	10	1.6	619	10	1945
Cell line (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	1.0e-05	10	1.6	619	10	1945
EWS/FLI expressing fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	1.0e-05	10	1.6	619	10	1945
Fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	1.0e-05	10	1.6	619	10	1945
Skin fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	1.0e-05	10	1.6	619	10	1945
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	1.4e-05	47	78.3	60	134	245
Atypical teratoid/rhabdoid tumour - CNS and other origin (Neuro tumors)	Neuro tumors	0.0001	8	36.3	22	10	90
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	0.0001	23	23	100	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	0.0001	23	23	100	205	1945
Normal tissue (Liver cancer)	Liver cancer	0.0001	8	25.8	31	14	207
Stage T1 (Lung cancer)	Lung cancer	0.0002	122	85.3	143	153	195
Cancer and cell line (Liver cancer)	Liver cancer	0.0002	23	92	25	126	207

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
organogenesis	5.4e-06	41	14.0	291	315	4566
development	6.8e-06	61	20.9	291	554	4566
morphogenesis	8.4e-06	45	15.4	291	366	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 719 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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