Module 345 -- Immune response and Ag processing and presentation

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:	129 (see 799 additional genes for this module)
Num experiments:	953 (441 induced, 512 repressed)
Parent module:	436
Children modules:	292 293

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.
antigen processing
antigen presentation, peptide antigen
MHC class I receptor activity
antigen processing, endogenous antigen via MHC class I
antigen presentation, endogenous antigen
Boldrick02 4
Boldrick02 18
Boldrick02 10
Boldrick02 36
Boldrick02 9
Alizadeh00 36
Rosenwald01 11
Rosenwald01 14
Alizadeh00 5
Perou00 29

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
Hematologic samples (Stimulated PBMC*)	Stimulated PBMC*	3.0e-49	116	26.3	441	152	1945
Lymphocytes (Stimulated PBMC*)	Stimulated PBMC*	3.0e-49	116	26.3	441	152	1945
Primary blood mononuclear cells (Stimulated PBMC*)	Stimulated PBMC*	3.0e-49	116	26.3	441	152	1945
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	2.6e-36	116	26.3	441	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	2.6e-36	116	26.3	441	182	1945
Stimulated immune cells (Stimulated PBMC*)	Stimulated PBMC*	7.6e-29	92	20.8	441	143	1945
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	1.4e-22	30	63.8	47	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	1.4e-22	30	63.8	47	30	182
Lung carcinoid (Lung cancer)	Lung cancer	2.1e-14	20	30.7	65	20	276
Cancer and cell line (Liver cancer)	Liver cancer	2.2e-14	64	95.5	67	126	207
Cancer (B lymphoma*)	B lymphoma*	4.2e-09	80	18.1	441	200	1945
Hematologic cancer (B lymphoma*)	B lymphoma*	4.2e-09	80	18.1	441	200	1945
B cells (B lymphoma*)	B lymphoma*	1.1e-08	88	19.9	441	231	1945
Liver tissue (Liver cancer*)	Liver cancer*	1.2e-08	75	17.0	441	187	1945
Acute leukemia (Leukemia*)	Leukemia*	1.5e-08	67	13.0	512	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	1.5e-08	67	13.0	512	141	1945
Cancer (Leukemia*)	Leukemia*	1.5e-08	67	13.0	512	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	1.5e-08	67	13.0	512	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	1.5e-08	67	13.0	512	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	1.5e-08	67	13.0	512	141	1945
Leukemia (Leukemia*)	Leukemia*	1.5e-08	67	13.0	512	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	1.5e-08	67	13.0	512	141	1945
Monocytes (Leukemia*)	Leukemia*	1.5e-08	67	13.0	512	141	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.3e-08	65	14.7	441	156	1945
Lymphocytes (B lymphoma*)	B lymphoma*	4.7e-08	90	20.4	441	244	1945
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	5.7e-08	30	85.7	35	67	144
Cancer and cell line (B lymphoma*)	B lymphoma*	1.6e-07	80	18.1	441	214	1945
Hematologic cancer and cell line (B lymphoma*)	B lymphoma*	1.6e-07	80	18.1	441	214	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.8e-07	75	17.0	441	197	1945
Activated B like DLBCL (B lymphoma)	B lymphoma	3.0e-07	24	26.6	90	30	245
Cell line (B lymphoma)	B lymphoma	3.8e-07	13	18.5	70	14	245
Diffuse large B cell lymphoma - DLBCL (Various tumors)	Various tumors	7.2e-07	6	75	8	11	154
Diffuse large B cell lymphoma tumor or cell line (Various tumors)	Various tumors	7.2e-07	6	75	8	11	154
Cancer (Liver cancer)	Liver cancer	1.4e-06	53	79.1	67	115	207
Lymphoma (Various tumors)	Various tumors	1.6e-06	7	87.5	8	20	154
Cell line (Liver cancer)	Liver cancer	2.2e-06	11	16.4	67	11	207
B cells (Various tumors)	Various tumors	4.9e-06	7	87.5	8	23	154
Liver cancer cell line (Liver cancer)	Liver cancer	7.7e-06	10	14.9	67	10	207
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	9.3e-06	30	85.7	35	78	144
CNS tissue, cancer or cell line (Various tumors)	Various tumors	1.7e-05	17	29.3	58	21	154
Lymphocytes (Various tumors)	Various tumors	2.3e-05	7	87.5	8	28	154
Monocytes (Various tumors)	Various tumors	2.3e-05	7	87.5	8	28	154
Cell line (Breast cancer)	Breast cancer	2.7e-05	19	41.3	46	30	152
Breast cancer cell line (Breast cancer)	Breast cancer	4.0e-05	13	28.2	46	17	152
Hematologic cancer and cell line (Various tumors)	Various tumors	5.0e-05	7	87.5	8	31	154
Hematologic cancer (Various tumors)	Various tumors	5.0e-05	7	87.5	8	31	154
Primary blood mononuclear cells (Various tumors)	Various tumors	5.0e-05	7	87.5	8	31	154
Non-tumor liver tissue (Liver cancer)	Liver cancer	8.7e-05	41	53.9	76	76	207
T cells (B lymphoma)	B lymphoma	0.0001	7	10	70	7	245
Adenocarcinoma (Breast cancer*)	Breast cancer*	0.0001	42	9.5	441	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	0.0001	42	9.5	441	112	1945
Cancer (Breast cancer*)	Breast cancer*	0.0001	42	9.5	441	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	0.0001	42	9.5	441	112	1945
Hematologic samples and cell lines (Various tumors)	Various tumors	0.0001	7	87.5	8	37	154
Hematologic samples (Various tumors)	Various tumors	0.0001	7	87.5	8	37	154
Breast tissue or cancer (NCI60)	NCI60	0.0002	4	21.0	19	4	139
Female hormonal tissue or cancer (NCI60)	NCI60	0.0002	4	21.0	19	4	139
Acute lymphocytic leukemia - MLL sub class (Leukemia)	Leukemia	0.0003	12	85.7	14	20	44
Breast tissue or cancer (Breast cancer*)	Breast cancer*	0.0003	43	9.7	441	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	0.0003	43	9.7	441	118	1945
Female hormonal cancer cell line (Breast cancer)	Breast cancer	0.0003	11	23.9	46	15	152
Slow doubling (60-80) cell lines (NCI60)	NCI60	0.0004	5	35.7	14	8	122

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	1.4e-21	40	65.5	61	600	4566
response to stress	4.8e-18	41	67.2	61	792	4566
immune response	1.0e-14	30	49.1	61	469	4566
receptor activity	5.7e-07	23	37.7	61	582	4566
signal transducer activity	1.0e-06	31	50.8	61	1026	4566
transmembrane receptor activity	2.8e-06	19	31.1	61	448	4566
antigen presentation\, peptide antigen	2.6e-05	4	6.5	61	14	4566
antigen processing	2.6e-05	4	6.5	61	14	4566
cellular defense response	4.4e-05	6	9.8	61	50	4566
response to pest/pathogen/parasite	4.7e-05	10	16.3	61	163	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 953 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

>4x