Module 129 -- 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:	9
Num genes:	219 (see 2163 additional genes for this module)
Num experiments:	850 (204 induced, 646 repressed)
Parent module:	None
Children modules:	99

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.
Singh02 26
Armstrong01 22
Bhattacharjee01 16
Armstrong01 37
Armstrong01 5
Armstrong01 6
Bhattacharjee01 24
Bhattacharjee01 6
Armstrong01 42

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*	5.4e-53	206	31.9	645	276	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	1.3e-48	189	29.3	645	252	1945
Cancer (Lung cancer*)	Lung cancer*	1.3e-48	189	29.3	645	252	1945
Lung cancer (Lung cancer*)	Lung cancer*	3.9e-45	178	27.5	645	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	3.9e-45	178	27.5	645	238	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	8.6e-40	155	24.0	645	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	8.6e-40	155	24.0	645	205	1945
Liver tissue (Liver cancer*)	Liver cancer*	2.9e-38	83	40.6	204	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	4.1e-36	83	40.6	204	197	1945
Acute leukemia (Leukemia*)	Leukemia*	1.0e-32	113	17.5	645	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	1.0e-32	113	17.5	645	141	1945
Cancer (Leukemia*)	Leukemia*	1.0e-32	113	17.5	645	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	1.0e-32	113	17.5	645	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	1.0e-32	113	17.5	645	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	1.0e-32	113	17.5	645	141	1945
Leukemia (Leukemia*)	Leukemia*	1.0e-32	113	17.5	645	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	1.0e-32	113	17.5	645	141	1945
Monocytes (Leukemia*)	Leukemia*	1.0e-32	113	17.5	645	141	1945
Cancer and cell line (Liver cancer)	Liver cancer	6.7e-28	87	100	87	126	207
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.6e-25	63	30.8	204	156	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	7.2e-25	65	77.3	84	76	207
Cancer (Liver cancer)	Liver cancer	3.5e-17	77	88.5	87	115	207
Hepatocellular carcinoma (Liver cancer)	Liver cancer	2.9e-11	67	77.0	87	104	207
Adenocarcinoma (Liver cancer)	Liver cancer	3.5e-11	64	73.5	87	97	207
Hematologic samples and cell lines (B lymphoma)	B lymphoma	7.5e-09	28	96.5	29	121	245
Lymphoma (B lymphoma)	B lymphoma	1.9e-08	23	79.3	29	77	245
Invasive liver tumor (Liver cancer)	Liver cancer	3.6e-07	30	34.4	87	38	207
Cancer and cell line (NCI60*)	NCI60*	5.5e-07	34	16.6	204	138	1945
Hematologic samples and cell lines (Various tumors)	Various tumors	9.2e-07	29	43.2	67	37	154
Hematologic samples (Various tumors)	Various tumors	9.2e-07	29	43.2	67	37	154
Normal tissue (Liver cancer)	Liver cancer	1.6e-06	14	16.6	84	14	207
Cell line (Breast cancer)	Breast cancer	3.6e-06	17	50	34	30	152
Cell line (NCI60*)	NCI60*	9.4e-06	31	15.1	204	135	1945
Breast tissue or cancer (Breast cancer*)	Breast cancer*	4.1e-05	27	13.2	204	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	4.1e-05	27	13.2	204	118	1945
Cancer and cell line (Various tumors*)	Various tumors*	5.3e-05	54	8.3	645	105	1945
Cancer (Various tumors*)	Various tumors*	5.3e-05	54	8.3	645	105	1945
Breast cancer cell line (Breast cancer)	Breast cancer	7.6e-05	11	32.3	34	17	152
Hematologic cancer and cell line (Various tumors)	Various tumors	0.0001	23	34.3	67	31	154
Hematologic cancer (Various tumors)	Various tumors	0.0001	23	34.3	67	31	154
Primary blood mononuclear cells (Various tumors)	Various tumors	0.0001	23	34.3	67	31	154
Liver cancer cell line (Liver cancer)	Liver cancer	0.0001	10	11.4	87	10	207
Female hormonal cancer cell line (Breast cancer)	Breast cancer	0.0001	10	29.4	34	15	152
Hematologic cancer and cell line (NCI60)	NCI60	0.0001	13	20.3	64	14	139
Hematologic samples and cell lines (NCI60)	NCI60	0.0001	13	20.3	64	14	139
Leukemia cell line (NCI60)	NCI60	0.0001	13	20.3	64	14	139
Fast doubling (20-40) cell lines (NCI60)	NCI60	0.0001	54	88.5	61	90	122
Adenocarcinoma (Breast cancer*)	Breast cancer*	0.0003	24	11.7	204	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	0.0003	24	11.7	204	112	1945
Cancer (Breast cancer*)	Breast cancer*	0.0003	24	11.7	204	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	0.0003	24	11.7	204	112	1945
Atypical teratoid/rhabdoid tumour - CNS and other origin (Neuro tumors)	Neuro tumors	0.0003	7	38.8	18	10	90
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	0.0004	28	13.7	204	141	1945

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).

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 850 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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