Module 84 -- Immune (humoral) and inflammatory 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:	15
Num genes:	552 (see 1962 additional genes for this module)
Num experiments:	1548 (498 induced, 1050 repressed)
Parent module:	None
Children modules:	45 44

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.
Spleen
Thymus_2
Thymus_1
Whole_Blood_6
Whole_Blood_3
Whole_Blood_4
Whole_Blood_1
Whole_Blood_5
Whole_Blood_2
Perou00 42
Bhattacharjee01 7
Perou00 18
Garber01 45
Chen02 50
Sorlie01 20

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*	8.7e-26	112	22.4	498	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	4.6e-23	112	22.4	498	197	1945
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	5.2e-23	30	65.2	46	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	5.2e-23	30	65.2	46	30	182
Cancer and cell line (Liver cancer)	Liver cancer	1.0e-20	81	96.4	84	126	207
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.4e-18	89	17.8	498	156	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	3.6e-18	70	61.9	113	76	207
Hematologic samples (Stimulated PBMC*)	Stimulated PBMC*	4.8e-18	87	17.4	498	152	1945
Lymphocytes (Stimulated PBMC*)	Stimulated PBMC*	4.8e-18	87	17.4	498	152	1945
Primary blood mononuclear cells (Stimulated PBMC*)	Stimulated PBMC*	4.8e-18	87	17.4	498	152	1945
Activated B like DLBCL (B lymphoma)	B lymphoma	9.5e-14	26	40.6	64	30	245
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	1.9e-12	44	34.3	128	46	245
Leukemia (B lymphoma)	B lymphoma	1.9e-12	44	34.3	128	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	1.9e-12	44	34.3	128	46	245
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	3.1e-12	56	87.5	64	126	245
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	8.5e-12	87	17.4	498	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	8.5e-12	87	17.4	498	182	1945
Prostate (Prostate cancer*)	Prostate cancer*	9.8e-12	86	8.1	1049	101	1945
Cancer (Liver cancer)	Liver cancer	1.0e-11	70	83.3	84	115	207
Cancer and cell line (Lung cancer*)	Lung cancer*	1.5e-10	182	17.3	1049	252	1945
Cancer (Lung cancer*)	Lung cancer*	1.5e-10	182	17.3	1049	252	1945
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	1.6e-10	56	87.5	64	134	245
Stimulated immune cells (Stimulated PBMC*)	Stimulated PBMC*	1.0e-09	69	13.8	498	143	1945
Acute leukemia (Leukemia*)	Leukemia*	2.2e-09	109	10.3	1049	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	2.2e-09	109	10.3	1049	141	1945
Cancer (Leukemia*)	Leukemia*	2.2e-09	109	10.3	1049	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	2.2e-09	109	10.3	1049	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	2.2e-09	109	10.3	1049	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	2.2e-09	109	10.3	1049	141	1945
Leukemia (Leukemia*)	Leukemia*	2.2e-09	109	10.3	1049	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	2.2e-09	109	10.3	1049	141	1945
Monocytes (Leukemia*)	Leukemia*	2.2e-09	109	10.3	1049	141	1945
Cancer and cell line (Various tumors*)	Various tumors*	2.6e-09	85	8.1	1049	105	1945
Cancer (Various tumors*)	Various tumors*	2.6e-09	85	8.1	1049	105	1945
Lung cancer (Lung cancer*)	Lung cancer*	3.1e-09	170	16.2	1049	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	3.1e-09	170	16.2	1049	238	1945
Acute lymphocytic leukemia (Leukemia)	Leukemia	5.5e-09	92	78.6	117	99	149
Lymphocytes (Leukemia)	Leukemia	2.2e-08	84	77.0	109	91	141
Hepatocellular carcinoma (Liver cancer)	Liver cancer	7.7e-08	61	72.6	84	104	207
Adenocarcinoma (Liver cancer)	Liver cancer	4.7e-07	57	67.8	84	97	207
Cell line (NCI60*)	NCI60*	5.1e-07	100	9.5	1049	135	1945
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	1.3e-06	28	82.3	34	67	144
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	1.7e-06	58	90.6	64	167	245
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	2.5e-06	184	17.5	1049	276	1945
Cancer and cell line (NCI60*)	NCI60*	2.9e-06	100	9.5	1049	138	1945
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	4.4e-06	29	5.8	498	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	4.4e-06	29	5.8	498	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	4.4e-06	29	5.8	498	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	4.4e-06	29	5.8	498	53	1945
Adenocarcinoma (Breast cancer*)	Breast cancer*	5.1e-06	50	10.0	498	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	5.1e-06	50	10.0	498	112	1945
Cancer (Breast cancer*)	Breast cancer*	5.1e-06	50	10.0	498	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	5.1e-06	50	10.0	498	112	1945
Breast tissue or cancer (Breast cancer*)	Breast cancer*	5.2e-06	52	10.4	498	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	5.2e-06	52	10.4	498	118	1945
Epithelial cell line (NCI60)	NCI60	7.0e-06	32	31.6	101	32	139
Breast cancer cell line (Breast cancer)	Breast cancer	1.2e-05	14	28	50	17	152
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	1.4e-05	139	13.2	1049	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	1.4e-05	139	13.2	1049	205	1945
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	1.8e-05	29	85.2	34	78	144
Cell line (Breast cancer)	Breast cancer	2.3e-05	20	40	50	30	152
B cells (Leukemia)	Leukemia	2.3e-05	58	53.2	109	62	141
Cell line (Liver cancer)	Liver cancer	3.2e-05	11	13.0	84	11	207
Malignant glioblastoma (Neuro tumors)	Neuro tumors	5.9e-05	6	60	10	10	90
Cell line (B lymphoma)	B lymphoma	7.8e-05	14	10.9	128	14	245
Liver cancer cell line (Liver cancer)	Liver cancer	8.6e-05	10	11.9	84	10	207
Female hormonal cancer cell line (Breast cancer)	Breast cancer	0.0001	12	24	50	15	152
GC B like DLBCL (B lymphoma)	B lymphoma	0.0001	25	39.0	64	53	245
Lung carcinoid (Lung cancer)	Lung cancer	0.0002	20	10.8	184	20	276
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	0.0002	50	10.0	498	127	1945
Breast cancer or cell line (Breast cancer*)	Breast cancer*	0.0003	50	10.0	498	128	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).
GO annotation	P-value	Hits	Hits(%)	Module genes	Genes in annotation	Genes
response to biotic stimulus	4.0e-33	135	36.2	372	600	4566
response to stress	1.0e-20	136	36.5	372	792	4566
immune response	1.4e-20	98	26.3	372	469	4566
inflammatory response	1.9e-13	35	9.4	372	108	4566
thermoregulation	1.4e-11	32	8.6	372	105	4566
response to pest/pathogen/parasite	1.7e-11	41	11.0	372	163	4566
defense/immunity protein activity	2.3e-08	27	7.2	372	103	4566
chemotaxis	1.6e-07	21	5.6	372	73	4566
energy taxis	2.0e-07	21	5.6	372	74	4566
chemokine receptor binding	2.1e-07	14	3.7	372	35	4566
taxis	3.4e-07	21	5.6	372	76	4566
receptor activity	5.6e-07	80	21.5	372	582	4566
extracellular space	6.7e-07	39	10.4	372	212	4566
cell communication	7.7e-07	123	33.0	372	1030	4566
cellular defense response	1.0e-06	16	4.3	372	50	4566
transmembrane receptor activity	1.2e-06	65	17.4	372	448	4566
interleukin binding	1.4e-06	11	2.9	372	25	4566
cell adhesion	2.2e-06	39	10.4	372	222	4566
signal transducer activity	3.6e-06	120	32.2	372	1026	4566
interleukin receptor activity	5.4e-06	11	2.9	372	28	4566
humoral immune response	5.8e-06	25	6.7	372	118	4566
hematopoietin/interferon-class (D200-domain) cytokine receptor activity	1.6e-05	13	3.4	372	42	4566
integral to plasma membrane	1.6e-05	78	20.9	372	612	4566
antiviral response protein activity	2.2e-05	8	2.1	372	17	4566
response to viruses	3.8e-05	8	2.1	372	18	4566
receptor binding	5.4e-05	37	9.9	372	235	4566
defense response	5.9e-05	41	11.0	372	272	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 552 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 1548 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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