Module 75 -- Immune response

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:	5
Num genes:	399 (see 2668 additional genes for this module)
Num experiments:	1302 (426 induced, 876 repressed)
Parent module:	None
Children modules:	46

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 stress
response to biotic stimulus
immune response
response to pest/pathogen/parasite
humoral 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*	2.0e-30	109	25.5	426	187	1945
Acute leukemia (Leukemia*)	Leukemia*	2.4e-28	124	14.1	875	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	2.4e-28	124	14.1	875	141	1945
Cancer (Leukemia*)	Leukemia*	2.4e-28	124	14.1	875	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	2.4e-28	124	14.1	875	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	2.4e-28	124	14.1	875	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	2.4e-28	124	14.1	875	141	1945
Leukemia (Leukemia*)	Leukemia*	2.4e-28	124	14.1	875	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	2.4e-28	124	14.1	875	141	1945
Monocytes (Leukemia*)	Leukemia*	2.4e-28	124	14.1	875	141	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.2e-27	109	25.5	426	197	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	1.8e-24	73	66.9	109	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
Cancer and cell line (Liver cancer)	Liver cancer	1.5e-21	80	97.5	82	126	207
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.1e-20	85	19.9	426	156	1945
Hematologic samples (Stimulated PBMC*)	Stimulated PBMC*	3.4e-18	80	18.7	426	152	1945
Lymphocytes (Stimulated PBMC*)	Stimulated PBMC*	3.4e-18	80	18.7	426	152	1945
Primary blood mononuclear cells (Stimulated PBMC*)	Stimulated PBMC*	3.4e-18	80	18.7	426	152	1945
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	1.8e-12	80	18.7	426	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	1.8e-12	80	18.7	426	182	1945
Cancer (Liver cancer)	Liver cancer	5.9e-12	69	84.1	82	115	207
Stimulated immune cells (Stimulated PBMC*)	Stimulated PBMC*	1.8e-10	64	15.0	426	143	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	1.9e-10	160	18.2	875	252	1945
Cancer (Lung cancer*)	Lung cancer*	1.9e-10	160	18.2	875	252	1945
Cancer and cell line (Various tumors*)	Various tumors*	3.6e-10	78	8.9	875	105	1945
Cancer (Various tumors*)	Various tumors*	3.6e-10	78	8.9	875	105	1945
Lung cancer (Lung cancer*)	Lung cancer*	4.2e-09	149	17.0	875	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	4.2e-09	149	17.0	875	238	1945
Activated B like DLBCL (B lymphoma)	B lymphoma	1.4e-08	19	39.5	48	30	245
Hepatocellular carcinoma (Liver cancer)	Liver cancer	3.2e-07	59	71.9	82	104	207
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	3.9e-07	40	83.3	48	126	245
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	4.8e-07	26	86.6	30	67	144
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	5.6e-07	162	18.5	875	276	1945
Breast tissue or cancer (Breast cancer*)	Breast cancer*	1.5e-06	48	11.2	426	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	1.5e-06	48	11.2	426	118	1945
Adenocarcinoma (Breast cancer*)	Breast cancer*	1.9e-06	46	10.7	426	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	1.9e-06	46	10.7	426	112	1945
Cancer (Breast cancer*)	Breast cancer*	1.9e-06	46	10.7	426	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	1.9e-06	46	10.7	426	112	1945
Adenocarcinoma (Liver cancer)	Liver cancer	2.0e-06	55	67.0	82	97	207
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	2.2e-06	27	6.3	426	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	2.2e-06	27	6.3	426	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	2.2e-06	27	6.3	426	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	2.2e-06	27	6.3	426	53	1945
Invasive liver tumor (Liver cancer)	Liver cancer	2.7e-06	28	34.1	82	38	207
Breast cancer cell line (Breast cancer)	Breast cancer	3.5e-06	14	30.4	46	17	152
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	3.6e-06	123	14.0	875	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	3.6e-06	123	14.0	875	205	1945
Cell line (Breast cancer)	Breast cancer	4.0e-06	20	43.4	46	30	152
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	4.3e-06	40	83.3	48	134	245
Cell line (Liver cancer)	Liver cancer	2.4e-05	11	13.4	82	11	207
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	3.4e-05	26	86.6	30	78	144
Female hormonal cancer cell line (Breast cancer)	Breast cancer	4.0e-05	12	26.0	46	15	152
Liver cancer cell line (Liver cancer)	Liver cancer	6.7e-05	10	12.1	82	10	207
Metastasis (Liver cancer)	Liver cancer	6.7e-05	10	12.1	82	10	207
Normal tissue (Liver cancer)	Liver cancer	8.2e-05	14	12.8	109	14	207
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	9.5e-05	46	10.7	426	127	1945
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	0.0001	32	29.6	108	46	245
Leukemia (B lymphoma)	B lymphoma	0.0001	32	29.6	108	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	0.0001	32	29.6	108	46	245
Breast cancer or cell line (Breast cancer*)	Breast cancer*	0.0001	46	10.7	426	128	1945
Hematologic samples and cell lines (B lymphoma)	B lymphoma	0.0001	68	62.9	108	121	245
Acute lymphocytic leukemia (Leukemia)	Leukemia	0.0001	95	71.9	132	99	149
After doxorubicin chemotherapy (Breast cancer)	Breast cancer	0.0002	15	88.2	17	21	38
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
Lymphocytes (Leukemia)	Leukemia	0.0003	87	70.1	124	91	141
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	0.0003	48	11.2	426	141	1945
B cells (Leukemia)	Leukemia	0.0003	61	49.1	124	62	141

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	371	92.9	399	600	4566
immune response	1.2e-230	287	71.9	399	469	4566
response to stress	6.5e-213	334	83.7	399	792	4566
defense response	2.9e-89	145	36.3	399	272	4566
response to pest/pathogen/parasite	2.3e-86	113	28.3	399	163	4566
humoral immune response	2.3e-60	81	20.3	399	118	4566
lymphocyte activation	2.5e-59	105	26.3	399	209	4566
T-cell activation	1.0e-58	104	26.0	399	207	4566
signal transducer activity	1.2e-45	213	53.3	399	1026	4566
receptor binding	1.5e-35	87	21.8	399	235	4566
defense/immunity protein activity	1.7e-33	56	14.0	399	103	4566
chemokine receptor binding	2.1e-31	32	8.0	399	35	4566
chemotaxis	2.8e-30	45	11.2	399	73	4566
energy taxis	6.7e-30	45	11.2	399	74	4566
inflammatory response	7.8e-30	54	13.5	399	108	4566
taxis	3.5e-29	45	11.2	399	76	4566
humoral defense mechanism (sensu Invertebrata)	3.9e-28	43	10.7	399	72	4566
cellular defense response	5.2e-28	36	9.0	399	50	4566
thermoregulation	2.0e-27	51	12.7	399	105	4566
complement activation	4.0e-26	25	6.2	399	26	4566
regulation of complement activation	4.7e-25	24	6.0	399	25	4566
receptor activity	8.6e-24	123	30.8	399	582	4566
transmembrane receptor activity	3.6e-23	104	26.0	399	448	4566
cell-cell signaling	9.5e-23	64	16.0	399	194	4566
complement activation\, classical pathway	7.3e-22	21	5.2	399	22	4566
cell communication	5.2e-21	170	42.6	399	1030	4566
signal transduction	3.9e-20	146	36.5	399	831	4566
secretion	2.7e-19	67	16.7	399	240	4566
extracellular space	5.4e-19	62	15.5	399	212	4566
complement activity	1.2e-17	17	4.2	399	18	4566
regulation of T-cell proliferation	9.4e-17	32	8.0	399	69	4566
lymphocyte proliferation	1.6e-16	32	8.0	399	70	4566
positive regulation of cell proliferation	5.3e-16	31	7.7	399	68	4566
cytokine activity	1.1e-14	28	7.0	399	61	4566
growth factor activity	7.8e-13	33	8.2	399	95	4566
complement activation\, alternative pathway	2.3e-11	10	2.5	399	10	4566
integral to plasma membrane	3.3e-11	100	25.0	399	612	4566
hematopoietin/interferon-class (D200-domain) cytokine receptor activity	3.6e-11	20	5.0	399	42	4566
response to extracellular stimulus	7.9e-11	86	21.5	399	500	4566
calcium ion homeostasis	2.2e-10	12	3.0	399	16	4566
antigen presentation\, peptide antigen	5.6e-10	11	2.7	399	14	4566
antigen processing	5.6e-10	11	2.7	399	14	4566
cell surface receptor linked signal transduction	1.2e-09	53	13.2	399	259	4566
interleukin receptor activity	1.3e-09	15	3.7	399	28	4566
response to viruses	1.9e-09	12	3.0	399	18	4566
interleukin binding	2.2e-09	14	3.5	399	25	4566
response to pathogenic bacteria	2.5e-09	9	2.2	399	10	4566
metal ion homeostasis	4.6e-09	15	3.7	399	30	4566
cation homeostasis	8.3e-09	15	3.7	399	31	4566
host-pathogen interaction	8.3e-09	43	10.7	399	198	4566
acute-phase response	1.2e-08	9	2.2	399	11	4566
cell ion homeostasis	2.4e-08	15	3.7	399	33	4566
MHC class I receptor activity	2.6e-08	8	2.0	399	9	4566
immunoglobulin receptor activity	2.8e-08	13	3.2	399	25	4566
cell death	7.4e-08	32	8.0	399	134	4566
death	1.1e-07	59	14.7	399	342	4566
antigen presentation\, endogenous antigen	2.7e-07	7	1.7	399	8	4566
antigen processing\, endogenous antigen via MHC class I	2.7e-07	7	1.7	399	8	4566
porin activity	1.4e-06	43	10.7	399	235	4566
cytolysis	1.7e-06	9	2.2	399	16	4566
lymphocyte antigen	2.7e-06	6	1.5	399	7	4566
antiviral response protein activity	3.5e-06	9	2.2	399	17	4566
Fc receptor activity	3.5e-06	7	1.7	399	10	4566
protein kinase activity	4.4e-06	24	6.0	399	102	4566
heterophilic cell adhesion	1.2e-05	14	3.5	399	44	4566
transmembrane receptor protein tyrosine kinase activity	1.3e-05	17	4.2	399	62	4566
conjugation without cellular fusion	1.3e-05	30	7.5	399	152	4566
heparin binding	1.9e-05	13	3.2	399	40	4566
tumor necrosis factor receptor binding	1.9e-05	7	1.7	399	12	4566
carbohydrate binding	2.2e-05	15	3.7	399	52	4566
transmembrane receptor protein kinase activity	4.9e-05	17	4.2	399	68	4566
antimicrobial peptide activity	5.0e-05	10	2.5	399	27	4566
innate immune response	5.7e-05	4	1.0	399	4	4566
glycosaminoglycan binding	5.9e-05	13	3.2	399	44	4566
coreceptor activity	6.6e-05	6	1.5	399	10	4566
G-protein chemoattractant receptor activity	7.3e-05	7	1.7	399	14	4566
response to starvation	7.3e-05	7	1.7	399	14	4566
sugar binding	7.6e-05	14	3.5	399	51	4566
antigen binding	9.0e-05	5	1.2	399	7	4566
interleukin-1\, Type I\, activating receptor activity	9.0e-05	5	1.2	399	7	4566
cellular morphogenesis	0.0001	8	2.0	399	19	4566
binding	0.0001	128	32.0	399	1103	4566
cytosolic calcium ion concentration elevation	0.0001	9	2.2	399	24	4566
feeding behavior	0.0001	7	1.7	399	15	4566
invasive growth	0.0001	7	1.7	399	15	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 1302 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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