Module 451

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:	10
Num genes:	33 (see 315 additional genes for this module)
Num experiments:	508 (204 induced, 304 repressed)
Parent module:	None
Children modules:	403

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.
Chen02 27
response to DNA damage stimulus
Perou00 45
Nicotinate_and_nicotinamide_metabolism
Benzoate_degradation
DNA dependent ATPase activity
ATPase activity, coupled
regulation of transcription by pheromones
Boldrick02 34
viral host cell process manipulation

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 cancer and cell line (Stimulated PBMC)	Stimulated PBMC	2.6e-32	30	93.7	32	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	2.6e-32	30	93.7	32	30	182
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	2.7e-17	36	57.1	63	46	245
Leukemia (B lymphoma)	B lymphoma	2.7e-17	36	57.1	63	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	2.7e-17	36	57.1	63	46	245
Non-tumor liver tissue (Liver cancer)	Liver cancer	3.5e-14	40	83.3	48	76	207
Normal lung tissue (Lung cancer)	Lung cancer	4.5e-10	18	30	60	22	276
Normal tissue (Lung cancer)	Lung cancer	1.7e-09	18	30	60	23	276
Cell line (B lymphoma)	B lymphoma	8.8e-09	10	41.6	24	14	245
Liver cancer cell line (Liver cancer)	Liver cancer	5.6e-08	9	31.0	29	10	207
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	8.0e-08	22	95.6	23	67	144
Cancer and cell line (Liver cancer)	Liver cancer	1.3e-07	29	100	29	126	207
Cell line (Liver cancer)	Liver cancer	2.8e-07	9	31.0	29	11	207
Breast tissue or cancer (NCI60)	NCI60	3.3e-07	4	80	5	4	139
Female hormonal tissue or cancer (NCI60)	NCI60	3.3e-07	4	80	5	4	139
Hematologic samples and cell lines (Various tumors)	Various tumors	1.6e-06	13	76.4	17	37	154
Hematologic samples (Various tumors)	Various tumors	1.6e-06	13	76.4	17	37	154
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	3.6e-06	22	95.6	23	78	144
Small cell lung cancer (Lung cancer)	Lung cancer	3.8e-06	7	25.9	27	10	276
B cells (B lymphoma*)	B lymphoma*	4.5e-06	61	20.0	304	231	1945
Lymphocytes (B lymphoma*)	B lymphoma*	6.9e-06	63	20.7	304	244	1945
Centroblasts (Various tumors)	Various tumors	9.1e-06	5	29.4	17	5	154
GC B like DLBCL (Various tumors)	Various tumors	9.1e-06	5	29.4	17	5	154
Breast cancer (NCI60)	NCI60	2.2e-05	3	60	5	3	139
Normal tissue (Various tumors)	Various tumors	4.2e-05	21	61.7	34	49	154
B. petrussis 537 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	6.9e-05	5	21.7	23	5	144
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	6.9e-05	5	21.7	23	5	144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	6.9e-05	5	21.7	23	5	144
Liver tissue (Liver cancer*)	Liver cancer*	0.0001	48	15.7	304	187	1945
Grade 3 (Breast cancer)	Breast cancer	0.0001	10	100	10	38	85
Cell line (Breast cancer)	Breast cancer	0.0002	12	50	24	30	152
Cancer (B lymphoma*)	B lymphoma*	0.0003	49	16.1	304	200	1945
Hematologic cancer (B lymphoma*)	B lymphoma*	0.0003	49	16.1	304	200	1945
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	0.0004	21	87.5	24	134	245
Breast tissue, cancer or cell line (NCI60)	NCI60	0.0004	5	100	5	31	139

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 DNA damage stimulus	1.5e-11	14	60.8	23	310	4566
regulation of cell cycle	1.9e-09	10	43.4	23	163	4566
viral host cell process manipulation	1.7e-08	8	34.7	23	102	4566
DNA metabolism	5.5e-08	9	39.1	23	169	4566
host-pathogen interaction	3.0e-06	8	34.7	23	198	4566
response to stress	3.4e-06	14	60.8	23	792	4566
DNA dependent DNA replication	1.0e-05	4	17.3	23	29	4566
DNA replication and chromosome cycle	1.0e-05	4	17.3	23	29	4566
nucleotidyltransferase activity	1.6e-05	10	43.4	23	425	4566
ATP binding	7.3e-05	9	39.1	23	399	4566
cytokinesis	8.9e-05	4	17.3	23	49	4566
protein amino acid phosphorylation	9.2e-05	7	30.4	23	230	4566
DNA replication	0.0001	4	17.3	23	52	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 508 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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