Module 76 -- 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:	2
Num genes:	81 (see 2877 additional genes for this module)
Num experiments:	883 (310 induced, 573 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.
thermoregulation
inflammatory 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
Non-tumor liver tissue (Liver cancer)	Liver cancer	1.1e-23	63	77.7	81	76	207
Liver tissue (Liver cancer*)	Liver cancer*	2.1e-21	81	26.1	310	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.3e-19	81	26.1	310	197	1945
Cancer and cell line (Liver cancer)	Liver cancer	3.4e-18	68	98.5	69	126	207
Cancer and cell line (Lung cancer*)	Lung cancer*	5.1e-16	131	22.9	572	252	1945
Cancer (Lung cancer*)	Lung cancer*	5.1e-16	131	22.9	572	252	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.5e-15	64	20.6	310	156	1945
Lung cancer (Lung cancer*)	Lung cancer*	3.1e-15	124	21.6	572	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	3.1e-15	124	21.6	572	238	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	7.8e-13	133	23.2	572	276	1945
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	2.3e-11	40	95.2	42	126	245
Acute lymphocytic leukemia (Leukemia)	Leukemia	2.4e-11	65	92.8	70	99	149
B cells (Leukemia)	Leukemia	9.5e-11	46	74.1	62	62	141
Lymphocytes (Leukemia)	Leukemia	3.7e-10	57	91.9	62	91	141
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	3.7e-10	40	95.2	42	134	245
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	4.7e-10	100	17.4	572	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	4.7e-10	100	17.4	572	205	1945
Hematologic samples (Stimulated PBMC*)	Stimulated PBMC*	4.8e-10	54	17.4	310	152	1945
Lymphocytes (Stimulated PBMC*)	Stimulated PBMC*	4.8e-10	54	17.4	310	152	1945
Primary blood mononuclear cells (Stimulated PBMC*)	Stimulated PBMC*	4.8e-10	54	17.4	310	152	1945
Cancer (Liver cancer)	Liver cancer	1.9e-09	58	84.0	69	115	207
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	1.2e-08	58	18.7	310	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	1.2e-08	58	18.7	310	182	1945
Cell line (Breast cancer)	Breast cancer	7.6e-08	19	54.2	35	30	152
Activated B like DLBCL (B lymphoma)	B lymphoma	1.0e-07	17	40.4	42	30	245
Stimulated immune cells (Stimulated PBMC*)	Stimulated PBMC*	1.3e-07	47	15.1	310	143	1945
Bone marrow (Leukemia)	Leukemia	3.7e-07	21	33.8	62	23	141
Adenocarcinoma (Liver cancer)	Liver cancer	7.1e-07	49	71.0	69	97	207
Breast cancer cell line (Breast cancer)	Breast cancer	8.4e-07	13	37.1	35	17	152
Cancer and cell line (Various tumors*)	Various tumors*	9.2e-07	54	9.4	572	105	1945
Cancer (Various tumors*)	Various tumors*	9.2e-07	54	9.4	572	105	1945
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	3.6e-06	30	34.8	86	46	245
Leukemia (B lymphoma)	B lymphoma	3.6e-06	30	34.8	86	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	3.6e-06	30	34.8	86	46	245
Hepatocellular carcinoma (Liver cancer)	Liver cancer	4.7e-06	50	72.4	69	104	207
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	5.2e-06	40	95.2	42	167	245
Female hormonal cancer cell line (Breast cancer)	Breast cancer	1.6e-05	11	31.4	35	15	152
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	8.0e-05	20	6.4	310	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	8.0e-05	20	6.4	310	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	8.0e-05	20	6.4	310	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	8.0e-05	20	6.4	310	53	1945
Cell line (Liver cancer)	Liver cancer	8.5e-05	10	14.4	69	11	207
Breast tissue or cancer (NCI60)	NCI60	9.1e-05	4	26.6	15	4	139
Female hormonal tissue or cancer (NCI60)	NCI60	9.1e-05	4	26.6	15	4	139
Cell line (B lymphoma)	B lymphoma	9.3e-05	12	13.9	86	14	245
Acute leukemia (Leukemia*)	Leukemia*	9.6e-05	62	10.8	572	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	9.6e-05	62	10.8	572	141	1945
Cancer (Leukemia*)	Leukemia*	9.6e-05	62	10.8	572	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	9.6e-05	62	10.8	572	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	9.6e-05	62	10.8	572	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	9.6e-05	62	10.8	572	141	1945
Leukemia (Leukemia*)	Leukemia*	9.6e-05	62	10.8	572	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	9.6e-05	62	10.8	572	141	1945
Monocytes (Leukemia*)	Leukemia*	9.6e-05	62	10.8	572	141	1945
Liver cancer cell line (Liver cancer)	Liver cancer	0.0002	9	13.0	69	10	207
Live bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0002	5	16.6	30	5	148

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
inflammatory response	9.3e-151	81	100	81	108	4566
thermoregulation	5.8e-141	78	96.2	81	105	4566
chemotaxis	6.1e-47	36	44.4	81	73	4566
energy taxis	1.1e-46	36	44.4	81	74	4566
taxis	4.2e-46	36	44.4	81	76	4566
chemokine receptor binding	2.2e-40	26	32.0	81	35	4566
response to biotic stimulus	9.7e-32	56	69.1	81	600	4566
response to stress	2.6e-26	57	70.3	81	792	4566
immune response	1.5e-25	46	56.7	81	469	4566
cell-cell signaling	1.6e-21	30	37.0	81	194	4566
response to pest/pathogen/parasite	2.6e-21	28	34.5	81	163	4566
receptor binding	3.9e-20	31	38.2	81	235	4566
secretion	9.3e-19	30	37.0	81	240	4566
signal transducer activity	1.6e-18	55	67.9	81	1026	4566
conjugation without cellular fusion	6.6e-13	20	24.6	81	152	4566
signal transduction	4.8e-12	42	51.8	81	831	4566
cell communication	1.8e-11	46	56.7	81	1030	4566
calcium ion homeostasis	7.9e-11	8	9.8	81	16	4566
G-protein coupled receptor protein signaling pathway	9.6e-11	22	27.1	81	245	4566
humoral immune response	1.2e-09	15	18.5	81	118	4566
defense/immunity protein activity	1.8e-09	14	17.2	81	103	4566
metal ion homeostasis	2.9e-08	8	9.8	81	30	4566
cation homeostasis	3.9e-08	8	9.8	81	31	4566
cell ion homeostasis	6.6e-08	8	9.8	81	33	4566
extracellular space	1.0e-07	17	20.9	81	212	4566
cytosolic calcium ion concentration elevation	1.1e-07	7	8.6	81	24	4566
response to extracellular stimulus	1.9e-07	26	32.0	81	500	4566
peptide receptor activity	3.6e-07	9	11.1	81	55	4566
humoral defense mechanism (sensu Invertebrata)	3.8e-07	10	12.3	81	72	4566
transmembrane receptor activity	3.9e-07	24	29.6	81	448	4566
response to viruses	4.0e-07	6	7.4	81	18	4566
cell motility	4.9e-07	12	14.8	81	113	4566
peptide receptor activity\, G-protein coupled	5.8e-07	9	11.1	81	58	4566
binding	5.9e-07	40	49.3	81	1103	4566
rhodopsin-like receptor activity	1.3e-06	13	16.0	81	147	4566
G-protein signaling\, coupled to IP3 second messenger (phospholipase C activating)	1.4e-06	8	9.8	81	48	4566
G-protein chemoattractant receptor activity	2.7e-06	5	6.1	81	14	4566
interleukin-1\, Type I\, activating receptor activity	3.0e-06	4	4.9	81	7	4566
interleukin binding	3.4e-06	6	7.4	81	25	4566
invasive growth	4.0e-06	5	6.1	81	15	4566
interleukin-1 receptor activity	6.0e-06	4	4.9	81	8	4566
G-protein coupled receptor activity	6.8e-06	13	16.0	81	170	4566
interleukin receptor activity	7.1e-06	6	7.4	81	28	4566
cellular morphogenesis	1.4e-05	5	6.1	81	19	4566
response to pathogenic bacteria	1.7e-05	4	4.9	81	10	4566
innate immune response	2.1e-05	3	3.7	81	4	4566
cellular defense response	2.2e-05	7	8.6	81	50	4566
acute-phase response	2.7e-05	4	4.9	81	11	4566
chemokine binding	2.7e-05	4	4.9	81	11	4566
sensory perception	3.7e-05	27	33.3	81	700	4566
receptor activity	4.0e-05	24	29.6	81	582	4566
chemosensory perception	6.8e-05	26	32.0	81	682	4566
hematopoietin/interferon-class (D200-domain) cytokine receptor activity	8.1e-05	6	7.4	81	42	4566
antimicrobial peptide activity	9.2e-05	5	6.1	81	27	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 883 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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