Module 436

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:	27
Num genes:	141 (see 669 additional genes for this module)
Num experiments:	944 (446 induced, 498 repressed)
Parent module:	None
Children modules:	361 345

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.
Rosenwald01 50
Alizadeh00 48
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
Alizadeh00 27
Rosenwald01 42
Alizadeh00 13
Rosenwald01 31
Rosenwald01 9
Alizadeh00 18
Rosenwald01 48
Alizadeh00 11
Rosenwald01 40
Alizadeh00 8

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*	2.9e-45	113	25.3	446	152	1945
Lymphocytes (Stimulated PBMC*)	Stimulated PBMC*	2.9e-45	113	25.3	446	152	1945
Primary blood mononuclear cells (Stimulated PBMC*)	Stimulated PBMC*	2.9e-45	113	25.3	446	152	1945
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	3.7e-33	113	25.3	446	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	3.7e-33	113	25.3	446	182	1945
Stimulated immune cells (Stimulated PBMC*)	Stimulated PBMC*	1.0e-26	90	20.1	446	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	1.0e-14	20	31.7	63	20	276
Cancer and cell line (Liver cancer)	Liver cancer	1.0e-13	65	94.2	69	126	207
Cancer (B lymphoma*)	B lymphoma*	2.0e-12	88	19.7	446	200	1945
Hematologic cancer (B lymphoma*)	B lymphoma*	2.0e-12	88	19.7	446	200	1945
B cells (B lymphoma*)	B lymphoma*	3.7e-12	97	21.7	446	231	1945
Lymphocytes (B lymphoma*)	B lymphoma*	9.6e-12	100	22.4	446	244	1945
Cancer and cell line (B lymphoma*)	B lymphoma*	1.9e-10	88	19.7	446	214	1945
Hematologic cancer and cell line (B lymphoma*)	B lymphoma*	1.9e-10	88	19.7	446	214	1945
Cell line (B lymphoma)	B lymphoma	3.5e-09	14	21.2	66	14	245
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	1.1e-08	36	36	100	46	245
Leukemia (B lymphoma)	B lymphoma	1.1e-08	36	36	100	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	1.1e-08	36	36	100	46	245
Liver tissue (Liver cancer*)	Liver cancer*	5.5e-08	74	16.5	446	187	1945
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	5.7e-08	30	85.7	35	67	144
Acute leukemia (Leukemia*)	Leukemia*	9.5e-08	64	12.8	498	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	9.5e-08	64	12.8	498	141	1945
Cancer (Leukemia*)	Leukemia*	9.5e-08	64	12.8	498	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	9.5e-08	64	12.8	498	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	9.5e-08	64	12.8	498	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	9.5e-08	64	12.8	498	141	1945
Leukemia (Leukemia*)	Leukemia*	9.5e-08	64	12.8	498	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	9.5e-08	64	12.8	498	141	1945
Monocytes (Leukemia*)	Leukemia*	9.5e-08	64	12.8	498	141	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.0e-07	64	14.3	446	156	1945
CNS tissue, cancer or cell line (Various tumors)	Various tumors	1.6e-07	17	37.7	45	21	154
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	6.9e-07	74	16.5	446	197	1945
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
Lymphoma (Various tumors)	Various tumors	1.6e-06	7	87.5	8	20	154
Cancer (Liver cancer)	Liver cancer	2.1e-06	54	78.2	69	115	207
Cell line (Liver cancer)	Liver cancer	3.1e-06	11	15.9	69	11	207
Activated B like DLBCL (B lymphoma)	B lymphoma	3.7e-06	24	24	100	30	245
B cells (Various tumors)	Various tumors	4.9e-06	7	87.5	8	23	154
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	9.3e-06	30	85.7	35	78	144
Liver cancer cell line (Liver cancer)	Liver cancer	1.0e-05	10	14.4	69	10	207
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
Adenocarcinoma (Breast cancer*)	Breast cancer*	4.6e-05	44	9.8	446	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	4.6e-05	44	9.8	446	112	1945
Cancer (Breast cancer*)	Breast cancer*	4.6e-05	44	9.8	446	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	4.6e-05	44	9.8	446	112	1945
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
CNS cancer or cell line (Various tumors)	Various tumors	8.2e-05	12	26.6	45	16	154
CNS tumor (Various tumors)	Various tumors	8.2e-05	12	26.6	45	16	154
Breast tissue or cancer (Breast cancer*)	Breast cancer*	8.9e-05	45	10.0	446	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	8.9e-05	45	10.0	446	118	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	0.0001	40	53.3	75	76	207
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	22.2	18	4	139
Female hormonal tissue or cancer (NCI60)	NCI60	0.0002	4	22.2	18	4	139
Cell line (NCI60*)	NCI60*	0.0002	53	10.6	498	135	1945
Metastasis (Liver cancer)	Liver cancer	0.0002	9	13.0	69	10	207
After doxorubicin chemotherapy (Breast cancer)	Breast cancer	0.0002	15	88.2	17	21	38
Slow doubling (60-80) cell lines (NCI60)	NCI60	0.0002	5	38.4	13	8	122
Female hormonal cancer cell line (Breast cancer)	Breast cancer	0.0003	11	23.9	46	15	152
Cancer and cell line (NCI60*)	NCI60*	0.0004	53	10.6	498	138	1945
Primary blood mononuclear cells (B lymphoma)	B lymphoma	0.0004	10	15.1	66	14	245

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	2.0e-19	37	63.7	58	600	4566
response to stress	3.1e-16	38	65.5	58	792	4566
immune response	1.7e-15	30	51.7	58	469	4566
receptor activity	4.0e-08	24	41.3	58	582	4566
signal transducer activity	2.3e-07	31	53.4	58	1026	4566
transmembrane receptor activity	2.4e-07	20	34.4	58	448	4566
antigen presentation\, peptide antigen	2.1e-05	4	6.8	58	14	4566
antigen processing	2.1e-05	4	6.8	58	14	4566
signal transduction	9.7e-05	23	39.6	58	831	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 944 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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