Module 42

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:	2
Num genes:	25 (see 1894 additional genes for this module)
Num experiments:	95 (40 induced, 55 repressed)
Parent module:	77
Children modules:	None

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.
NADH dehydrogenase activity
NADH dehydrogenase (ubiquinone) activity

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
Prostate (Prostate cancer*)	Prostate cancer*	6.3e-18	24	43.6	55	101	1945
Lung carcinoid (Lung cancer)	Lung cancer	1.4e-09	8	88.8	9	20	276
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	8.3e-09	12	21.8	55	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	8.3e-09	12	21.8	55	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	8.3e-09	12	21.8	55	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	8.3e-09	12	21.8	55	53	1945
Cancer and cell line (Gliomas*)	Gliomas*	0.0002	7	12.7	55	47	1945
Cancer (Gliomas*)	Gliomas*	0.0002	7	12.7	55	47	1945
CNS cancer or cell line (Gliomas*)	Gliomas*	0.0002	7	12.7	55	47	1945
CNS tissue, cancer or cell line (Gliomas*)	Gliomas*	0.0002	7	12.7	55	47	1945
CNS tumor (Gliomas*)	Gliomas*	0.0002	7	12.7	55	47	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
NADH dehydrogenase (ubiquinone) activity	1.3e-65	25	100	25	26	4566
NADH dehydrogenase activity	6.1e-62	24	96	25	25	4566
sodium ion transporter activity	6.8e-53	25	100	25	50	4566
metal ion transporter activity	2.7e-50	25	100	25	60	4566
monovalent inorganic cation transporter activity	1.9e-46	25	100	25	80	4566
ion transporter activity	3.4e-39	25	100	25	144	4566
oxidoreductase activity	1.3e-32	25	100	25	254	4566
mitochondrion	3.6e-32	24	96	25	207	4566
electron transporter activity	6.0e-32	25	100	25	269	4566
mitochondrial electron transport\, NADH to ubiquinone	1.2e-30	13	52	25	14	4566
ATP synthesis coupled electron transport (sensu Eukarya)	9.1e-30	13	52	25	15	4566
protein-disulfide reduction	4.8e-29	13	52	25	16	4566
oxidative phosphorylation	2.0e-28	13	52	25	17	4566
membrane fraction	4.2e-15	17	68	25	304	4566
electron transport	1.3e-14	13	52	25	128	4566
phosphorus metabolism	3.8e-14	13	52	25	138	4566
phosphate metabolism	1.4e-13	13	52	25	153	4566
phosphorylation	9.2e-13	13	52	25	176	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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