Module 170 -- 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:	4
Num genes:	101 (see 2153 additional genes for this module)
Num experiments:	1043 (432 induced, 611 repressed)
Parent module:	None
Children modules:	128

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.
Alizadeh00 29
Rosenwald01 6
Alizadeh00 25
Rosenwald01 34

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
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	4.3e-24	71	97.2	73	126	245
Hematologic samples (Stimulated PBMC*)	Stimulated PBMC*	1.0e-22	87	20.1	432	152	1945
Lymphocytes (Stimulated PBMC*)	Stimulated PBMC*	1.0e-22	87	20.1	432	152	1945
Primary blood mononuclear cells (Stimulated PBMC*)	Stimulated PBMC*	1.0e-22	87	20.1	432	152	1945
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	2.0e-21	71	97.2	73	134	245
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	1.5e-19	93	21.5	432	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	1.5e-19	93	21.5	432	182	1945
Stimulated immune cells (Stimulated PBMC*)	Stimulated PBMC*	2.8e-15	73	16.8	432	143	1945
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	4.3e-14	44	36.9	119	46	245
Leukemia (B lymphoma)	B lymphoma	4.3e-14	44	36.9	119	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	4.3e-14	44	36.9	119	46	245
Activated B like DLBCL (B lymphoma)	B lymphoma	2.2e-13	27	36.9	73	30	245
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	1.5e-12	71	97.2	73	167	245
Cancer and cell line (Liver cancer)	Liver cancer	1.8e-12	58	95.0	61	126	207
Lung carcinoid (Lung cancer)	Lung cancer	1.9e-12	20	25.3	79	20	276
Acute lymphocytic leukemia (Leukemia)	Leukemia	2.9e-12	65	94.2	69	99	149
B cells (Leukemia)	Leukemia	3.0e-11	46	75.4	61	62	141
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	4.3e-11	24	48	50	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	4.3e-11	24	48	50	30	182
Lymphocytes (Leukemia)	Leukemia	5.2e-11	57	93.4	61	91	141
Non-tumor liver tissue (Liver cancer)	Liver cancer	3.7e-10	46	66.6	69	76	207
Lymphocytes (B lymphoma*)	B lymphoma*	1.8e-09	118	19.3	609	244	1945
Cell line (Breast cancer)	Breast cancer	6.1e-09	20	57.1	35	30	152
Hematologic samples (B lymphoma)	B lymphoma	4.2e-08	22	18.4	119	22	245
Breast cancer cell line (Breast cancer)	Breast cancer	4.5e-08	14	40	35	17	152
Normal lymphocytes (B lymphoma)	B lymphoma	2.4e-07	28	23.5	119	31	245
B cells (B lymphoma*)	B lymphoma*	2.4e-07	107	17.5	609	231	1945
Cell line (NCI60*)	NCI60*	5.4e-07	69	11.3	609	135	1945
Female hormonal cancer cell line (Breast cancer)	Breast cancer	1.1e-06	12	34.2	35	15	152
Cancer and cell line (NCI60*)	NCI60*	1.5e-06	69	11.3	609	138	1945
Liver tissue (Liver cancer*)	Liver cancer*	2.3e-06	68	15.7	432	187	1945
Liver cancer cell line (Liver cancer)	Liver cancer	2.8e-06	10	16.3	61	10	207
GC B like DLBCL (B lymphoma)	B lymphoma	3.3e-06	30	41.0	73	53	245
Bone marrow (Leukemia)	Leukemia	3.5e-06	20	32.7	61	23	141
Cancer (B lymphoma*)	B lymphoma*	3.8e-06	71	16.4	432	200	1945
Hematologic cancer (B lymphoma*)	B lymphoma*	3.8e-06	71	16.4	432	200	1945
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	7.5e-06	30	76.9	39	67	144
Cancer (Liver cancer)	Liver cancer	9.4e-06	48	78.6	61	115	207
Normal lung tissue (Lung cancer)	Lung cancer	1.6e-05	13	24.5	53	22	276
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.9e-05	68	15.7	432	197	1945
Cell line (Liver cancer)	Liver cancer	2.3e-05	10	16.3	61	11	207
Cell line (B lymphoma)	B lymphoma	2.6e-05	14	11.7	119	14	245
Primary blood mononuclear cells (B lymphoma)	B lymphoma	2.6e-05	14	11.7	119	14	245
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	2.8e-05	32	82.0	39	78	144
Normal tissue (Lung cancer)	Lung cancer	3.1e-05	13	24.5	53	23	276
Cancer and cell line (B lymphoma*)	B lymphoma*	5.7e-05	71	16.4	432	214	1945
Hematologic cancer and cell line (B lymphoma*)	B lymphoma*	5.7e-05	71	16.4	432	214	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	6.9e-05	55	12.7	432	156	1945
Fast doubling (20-40) cell lines (NCI60)	NCI60	0.0001	58	87.8	66	90	122
Stimulated B cells (B lymphoma)	B lymphoma	0.0001	12	10.0	119	12	245
Cancer and cell line (B lymphoma*)	B lymphoma*	0.0001	91	14.9	609	214	1945
Hematologic cancer and cell line (B lymphoma*)	B lymphoma*	0.0001	91	14.9	609	214	1945
Normal female hormonal tissue and cells (Various tumors)	Various tumors	0.0002	5	33.3	15	8	154
Normal female hormonal tissue (Various tumors)	Various tumors	0.0002	5	33.3	15	8	154

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	8.4e-14	18	23.0	78	108	4566
thermoregulation	7.4e-13	17	21.7	78	105	4566
response to biotic stimulus	4.0e-12	35	44.8	78	600	4566
response to stress	2.6e-09	36	46.1	78	792	4566
immune response	4.5e-09	27	34.6	78	469	4566
chemotaxis	2.6e-08	11	14.1	78	73	4566
energy taxis	3.0e-08	11	14.1	78	74	4566
taxis	4.1e-08	11	14.1	78	76	4566
chemokine receptor binding	1.4e-06	7	8.9	78	35	4566
cellular defense response	1.7e-05	7	8.9	78	50	4566
chemokine binding	2.3e-05	4	5.1	78	11	4566
G-protein chemoattractant receptor activity	6.9e-05	4	5.1	78	14	4566
invasive growth	9.3e-05	4	5.1	78	15	4566
calcium ion homeostasis	0.0001	4	5.1	78	16	4566
metal ion homeostasis	0.0001	5	6.4	78	30	4566
transmembrane receptor activity	0.0001	19	24.3	78	448	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 1043 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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