Module 95

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:	566 (see 2458 additional genes for this module)
Num experiments:	458 (205 induced, 253 repressed)
Parent module:	163
Children modules:	49 48

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.
Cuadras02 35
Garber01 10
Chen02 33
Detweiler01 13
Garber01 49
Whitfield02 22
Whitfield02 46
Chen02 8
Whitfield02 49
Detweiler01 23

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-47	101	39.9	253	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	7.8e-46	102	40.3	253	197	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	5.7e-34	81	39.5	205	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.4e-31	77	30.4	253	156	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	6.3e-28	66	32.1	205	156	1945
Liver tissue (Liver cancer*)	Liver cancer*	1.5e-27	72	35.1	205	187	1945
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	5.9e-12	25	12.1	205	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	5.9e-12	25	12.1	205	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	5.9e-12	25	12.1	205	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	5.9e-12	25	12.1	205	53	1945
Stage T2 (Lung cancer)	Lung cancer	3.4e-05	12	54.5	22	35	195
Cancer and cell line (HeLa cell cycle*)	HeLa cell cycle*	0.0002	22	10.7	205	96	1945
Cell line (HeLa cell cycle*)	HeLa cell cycle*	0.0002	22	10.7	205	96	1945
Epithelial cell line (HeLa cell cycle*)	HeLa cell cycle*	0.0002	22	10.7	205	96	1945
HeLa cell line (HeLa cell cycle*)	HeLa cell cycle*	0.0002	22	10.7	205	96	1945
Prostate (Various tumors)	Various tumors	0.0003	6	37.5	16	12	154

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).

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 566 genes, this image does not display the individual gene names, but rather condenses each gene 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.

Note: Since there are 458 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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