Module 46

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:	395 (see 2936 additional genes for this module)
Num experiments:	1240 (399 induced, 841 repressed)
Parent module:	75
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.
response to biotic stimulus
immune response

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*	4.2e-30	105	26.3	399	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.8e-27	105	26.3	399	197	1945
Acute leukemia (Leukemia*)	Leukemia*	1.9e-27	121	14.3	841	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	1.9e-27	121	14.3	841	141	1945
Cancer (Leukemia*)	Leukemia*	1.9e-27	121	14.3	841	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	1.9e-27	121	14.3	841	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	1.9e-27	121	14.3	841	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	1.9e-27	121	14.3	841	141	1945
Leukemia (Leukemia*)	Leukemia*	1.9e-27	121	14.3	841	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	1.9e-27	121	14.3	841	141	1945
Monocytes (Leukemia*)	Leukemia*	1.9e-27	121	14.3	841	141	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	1.2e-24	72	68.5	105	76	207
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	1.8e-23	30	66.6	45	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	1.8e-23	30	66.6	45	30	182
Hematologic samples (Stimulated PBMC*)	Stimulated PBMC*	6.9e-21	81	20.3	399	152	1945
Lymphocytes (Stimulated PBMC*)	Stimulated PBMC*	6.9e-21	81	20.3	399	152	1945
Primary blood mononuclear cells (Stimulated PBMC*)	Stimulated PBMC*	6.9e-21	81	20.3	399	152	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.2e-20	82	20.5	399	156	1945
Cancer and cell line (Liver cancer)	Liver cancer	2.6e-20	77	97.4	79	126	207
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	9.5e-15	81	20.3	399	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	9.5e-15	81	20.3	399	182	1945
Stimulated immune cells (Stimulated PBMC*)	Stimulated PBMC*	5.6e-13	66	16.5	399	143	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	8.6e-12	159	18.9	841	252	1945
Cancer (Lung cancer*)	Lung cancer*	8.6e-12	159	18.9	841	252	1945
Cancer (Liver cancer)	Liver cancer	6.6e-11	66	83.5	79	115	207
Lung cancer (Lung cancer*)	Lung cancer*	1.1e-10	149	17.7	841	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	1.1e-10	149	17.7	841	238	1945
Cancer and cell line (Various tumors*)	Various tumors*	5.0e-10	76	9.0	841	105	1945
Cancer (Various tumors*)	Various tumors*	5.0e-10	76	9.0	841	105	1945
Activated B like DLBCL (B lymphoma)	B lymphoma	3.6e-09	18	45	40	30	245
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	1.8e-08	162	19.2	841	276	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	2.5e-07	123	14.6	841	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	2.5e-07	123	14.6	841	205	1945
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	4.8e-07	26	86.6	30	67	144
Hepatocellular carcinoma (Liver cancer)	Liver cancer	5.6e-07	57	72.1	79	104	207
Cell line (Breast cancer)	Breast cancer	9.1e-07	20	46.5	43	30	152
Breast cancer cell line (Breast cancer)	Breast cancer	1.2e-06	14	32.5	43	17	152
Breast tissue or cancer (Breast cancer*)	Breast cancer*	1.5e-06	46	11.5	399	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	1.5e-06	46	11.5	399	118	1945
Adenocarcinoma (Breast cancer*)	Breast cancer*	2.0e-06	44	11.0	399	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	2.0e-06	44	11.0	399	112	1945
Cancer (Breast cancer*)	Breast cancer*	2.0e-06	44	11.0	399	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	2.0e-06	44	11.0	399	112	1945
Adenocarcinoma (Liver cancer)	Liver cancer	3.9e-06	53	67.0	79	97	207
Invasive liver tumor (Liver cancer)	Liver cancer	5.7e-06	27	34.1	79	38	207
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	1.0e-05	33	82.5	40	126	245
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	1.2e-05	32	32	100	46	245
Leukemia (B lymphoma)	B lymphoma	1.2e-05	32	32	100	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	1.2e-05	32	32	100	46	245
Cell line (Liver cancer)	Liver cancer	1.5e-05	11	13.9	79	11	207
Female hormonal cancer cell line (Breast cancer)	Breast cancer	1.7e-05	12	27.9	43	15	152
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	3.4e-05	26	86.6	30	78	144
Liver cancer cell line (Liver cancer)	Liver cancer	4.5e-05	10	12.6	79	10	207
Normal tissue (Liver cancer)	Liver cancer	4.7e-05	14	13.3	105	14	207
B cells (Leukemia)	Leukemia	5.9e-05	61	50.4	121	62	141
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	6.5e-05	33	82.5	40	134	245
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	8.7e-05	44	11.0	399	127	1945
Breast cancer or cell line (Breast cancer*)	Breast cancer*	0.0001	44	11.0	399	128	1945
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	0.0001	23	5.7	399	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	0.0001	23	5.7	399	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	0.0001	23	5.7	399	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	0.0001	23	5.7	399	53	1945
Squamous cell lung cancer (Lung cancer)	Lung cancer	0.0002	30	18.5	162	35	276
B. petrussis 537 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0002	5	16.6	30	5	144
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0002	5	16.6	30	5	144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0002	5	16.6	30	5	144
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	0.0003	46	11.5	399	141	1945
Breast tissue, cancer or cell line (Breast cancer*)	Breast cancer*	0.0003	46	11.5	399	142	1945
Acute lymphocytic leukemia (Leukemia)	Leukemia	0.0003	93	72.0	129	99	149

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	0	395	100	395	600	4566
immune response	5.9e-264	304	76.9	395	469	4566
response to stress	1.8e-201	325	82.2	395	792	4566
defense response	2.0e-104	156	39.4	395	272	4566
response to pest/pathogen/parasite	1.6e-99	121	30.6	395	163	4566
lymphocyte activation	2.4e-69	113	28.6	395	209	4566
T-cell activation	1.0e-68	112	28.3	395	207	4566
humoral immune response	2.9e-68	86	21.7	395	118	4566
signal transducer activity	5.6e-48	215	54.4	395	1026	4566
defense/immunity protein activity	9.2e-40	61	15.4	395	103	4566
receptor binding	1.6e-39	91	23.0	395	235	4566
humoral defense mechanism (sensu Invertebrata)	1.7e-33	47	11.8	395	72	4566
chemokine receptor binding	1.5e-31	32	8.1	395	35	4566
inflammatory response	3.7e-31	55	13.9	395	108	4566
chemotaxis	1.8e-30	45	11.3	395	73	4566
energy taxis	4.2e-30	45	11.3	395	74	4566
cellular defense response	1.1e-29	37	9.3	395	50	4566
taxis	2.2e-29	45	11.3	395	76	4566
thermoregulation	1.0e-28	52	13.1	395	105	4566
cell-cell signaling	4.7e-27	69	17.4	395	194	4566
complement activation	3.1e-26	25	6.3	395	26	4566
receptor activity	5.9e-26	126	31.8	395	582	4566
transmembrane receptor activity	2.2e-25	107	27.0	395	448	4566
regulation of complement activation	3.7e-25	24	6.0	395	25	4566
secretion	8.7e-24	73	18.4	395	240	4566
signal transduction	1.4e-22	150	37.9	395	831	4566
cell communication	1.6e-22	172	43.5	395	1030	4566
regulation of T-cell proliferation	3.4e-22	37	9.3	395	69	4566
complement activation\, classical pathway	5.8e-22	21	5.3	395	22	4566
lymphocyte proliferation	6.7e-22	37	9.3	395	70	4566
positive regulation of cell proliferation	2.3e-21	36	9.1	395	68	4566
extracellular space	3.1e-19	62	15.6	395	212	4566
cytokine activity	7.5e-18	31	7.8	395	61	4566
complement activity	1.0e-17	17	4.3	395	18	4566
growth factor activity	2.0e-15	36	9.1	395	95	4566
integral to plasma membrane	1.6e-13	105	26.5	395	612	4566
response to viruses	2.3e-12	14	3.5	395	18	4566
complement activation\, alternative pathway	2.1e-11	10	2.5	395	10	4566
hematopoietin/interferon-class (D200-domain) cytokine receptor activity	2.9e-11	20	5.0	395	42	4566
response to extracellular stimulus	1.1e-10	85	21.5	395	500	4566
host-pathogen interaction	1.5e-10	46	11.6	395	198	4566
calcium ion homeostasis	1.9e-10	12	3.0	395	16	4566
acute-phase response	2.1e-10	10	2.5	395	11	4566
antigen presentation\, peptide antigen	5.1e-10	11	2.7	395	14	4566
antigen processing	5.1e-10	11	2.7	395	14	4566
cell surface receptor linked signal transduction	8.8e-10	53	13.4	395	259	4566
immunoglobulin receptor activity	1.9e-09	14	3.5	395	25	4566
response to pathogenic bacteria	2.3e-09	9	2.2	395	10	4566
metal ion homeostasis	4.0e-09	15	3.7	395	30	4566
cation homeostasis	7.2e-09	15	3.7	395	31	4566
interleukin receptor activity	1.3e-08	14	3.5	395	28	4566
cell ion homeostasis	2.1e-08	15	3.7	395	33	4566
MHC class I receptor activity	2.4e-08	8	2.0	395	9	4566
interleukin binding	2.4e-08	13	3.2	395	25	4566
cell death	5.8e-08	32	8.1	395	134	4566
conjugation without cellular fusion	1.2e-07	34	8.6	395	152	4566
death	1.9e-07	58	14.6	395	342	4566
antiviral response protein activity	2.3e-07	10	2.5	395	17	4566
antigen presentation\, endogenous antigen	2.5e-07	7	1.7	395	8	4566
antigen processing\, endogenous antigen via MHC class I	2.5e-07	7	1.7	395	8	4566
antimicrobial peptide activity	7.8e-07	12	3.0	395	27	4566
tumor necrosis factor receptor binding	1.0e-06	8	2.0	395	12	4566
cytolysis	1.6e-06	9	2.2	395	16	4566
heterophilic cell adhesion	1.9e-06	15	3.7	395	44	4566
antigen binding	2.6e-06	6	1.5	395	7	4566
lymphocyte antigen	2.6e-06	6	1.5	395	7	4566
porin activity	2.8e-06	42	10.6	395	235	4566
heparin binding	2.9e-06	14	3.5	395	40	4566
Fc receptor activity	3.2e-06	7	1.7	395	10	4566
carbohydrate binding	4.0e-06	16	4.0	395	52	4566
antibacterial peptide activity	9.7e-06	6	1.5	395	8	4566
glycosaminoglycan binding	1.0e-05	14	3.5	395	44	4566
binding	1.4e-05	131	33.1	395	1103	4566
sugar binding	1.5e-05	15	3.7	395	51	4566
transmembrane receptor protein tyrosine kinase signaling protein activity	1.8e-05	17	4.3	395	64	4566
G-protein coupled receptor protein signaling pathway	4.5e-05	40	10.1	395	245	4566
innate immune response	5.5e-05	4	1.0	395	4	4566
coreceptor activity	6.2e-05	6	1.5	395	10	4566
G-protein chemoattractant receptor activity	6.9e-05	7	1.7	395	14	4566
response to starvation	6.9e-05	7	1.7	395	14	4566
interleukin-1\, Type I\, activating receptor activity	8.5e-05	5	1.2	395	7	4566
cellular morphogenesis	9.3e-05	8	2.0	395	19	4566
cytosolic calcium ion concentration elevation	9.9e-05	9	2.2	395	24	4566
feeding behavior	0.0001	7	1.7	395	15	4566
invasive growth	0.0001	7	1.7	395	15	4566
viral host cell process manipulation	0.0001	21	5.3	395	102	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 1240 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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