Module 318

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:	28 (see 924 additional genes for this module)
Num experiments:	70 (39 induced, 31 repressed)
Parent module:	403
Children modules:	229

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.
DNA dependent ATPase activity
ATPase activity, coupled
regulation of transcription by pheromones
Boldrick02 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
Liver tissue (Liver cancer*)	Liver cancer*	1.2e-05	12	38.7	31	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	2.0e-05	12	38.7	31	197	1945
Liver cancer cell line (Liver cancer)	Liver cancer	3.4e-05	5	45.4	11	10	207
Cell line (Liver cancer)	Liver cancer	6.0e-05	5	45.4	11	11	207
Hepatitis infected liver (Liver cancer*)	Liver cancer*	8.3e-05	10	32.2	31	156	1945
Fibroblasts (Fibroblast serum*)	Fibroblast serum*	0.0001	4	12.9	31	17	1945
Cancer and cell line (Fibroblast serum*)	Fibroblast serum*	0.0001	4	12.9	31	18	1945
Cell line (Fibroblast serum*)	Fibroblast serum*	0.0001	4	12.9	31	18	1945
Skin fibroblasts (Fibroblast serum*)	Fibroblast serum*	0.0001	4	12.9	31	18	1945

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
DNA dependent ATPase activity	1.7e-39	19	67.8	28	28	4566
ATPase activity\, coupled	6.7e-23	14	50	28	41	4566
ATP binding	2.3e-17	21	75	28	399	4566
ATP dependent DNA helicase activity	1.0e-16	8	28.5	28	11	4566
hydrolase activity\, acting on acid anhydrides\, in phosphorus-containing anhydrides	8.0e-16	14	50	28	118	4566
primary active transporter activity	5.1e-15	7	25	28	9	4566
nucleotidyltransferase activity	5.4e-14	19	67.8	28	425	4566
P-P-bond-hydrolysis-driven transporter activity	1.1e-13	7	25	28	12	4566
DNA metabolism	1.3e-13	14	50	28	169	4566
nucleus	4.3e-13	24	85.7	28	966	4566
endomembrane system	1.8e-12	24	85.7	28	1029	4566
DNA repair	2.2e-12	11	39.2	28	93	4566
DNA recombination	1.1e-10	7	25	28	27	4566
regulation of transcription from Pol II promoter	6.5e-09	10	35.7	28	146	4566
regulation of transcription by pheromones	2.5e-08	9	32.1	28	123	4566
DNA binding	4.1e-08	13	46.4	28	357	4566
damaged DNA binding	2.3e-07	5	17.8	28	24	4566
RNA dependent ATPase activity	6.3e-07	5	17.8	28	29	4566
carrier activity	8.9e-07	9	32.1	28	186	4566
regulation of transcription\, DNA-dependent	2.4e-06	14	50	28	595	4566
response to DNA damage stimulus	7.8e-06	10	35.7	28	310	4566
ATP dependent helicase activity	1.1e-05	4	14.2	28	24	4566
meiotic recombination	1.1e-05	3	10.7	28	8	4566
catalytic activity	4.0e-05	21	75	28	1677	4566
hydrolase activity	6.3e-05	14	50	28	783	4566
chemosensory perception	7.0e-05	13	46.4	28	682	4566
sensory perception	9.2e-05	13	46.4	28	700	4566
transcription regulator activity	9.6e-05	13	46.4	28	703	4566
phosphotransferase activity\, alcohol group as acceptor	0.0001	5	17.8	28	82	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.

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