Module 287

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:	50 (see 1405 additional genes for this module)
Num experiments:	228 (90 induced, 138 repressed)
Parent module:	373
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.
vision
perception of light

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-15	36	40.4	89	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	7.6e-15	36	40.4	89	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	3.3e-11	28	31.4	89	156	1945
Cancer and cell line (Liver cancer)	Liver cancer	2.4e-10	39	100	39	126	207
B cells (Leukemia)	Leukemia	4.4e-08	25	89.2	28	62	141
Acute leukemia (Leukemia*)	Leukemia*	1.6e-07	28	20.2	138	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	1.6e-07	28	20.2	138	141	1945
Cancer (Leukemia*)	Leukemia*	1.6e-07	28	20.2	138	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	1.6e-07	28	20.2	138	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	1.6e-07	28	20.2	138	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	1.6e-07	28	20.2	138	141	1945
Leukemia (Leukemia*)	Leukemia*	1.6e-07	28	20.2	138	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	1.6e-07	28	20.2	138	141	1945
Monocytes (Leukemia*)	Leukemia*	1.6e-07	28	20.2	138	141	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	2.2e-07	34	24.6	138	197	1945
Cancer and cell line (NCI60*)	NCI60*	3.5e-07	21	23.5	89	138	1945
Cell line (NCI60*)	NCI60*	1.1e-06	20	22.4	89	135	1945
Cancer (Liver cancer)	Liver cancer	4.2e-06	34	87.1	39	115	207
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.6e-05	26	18.8	138	156	1945
Liver tissue (Liver cancer*)	Liver cancer*	2.0e-05	29	21.0	138	187	1945
Primary blood mononuclear cells (Leukemia)	Leukemia	3.6e-05	12	42.8	28	21	141
Cell line (Breast cancer)	Breast cancer	7.7e-05	10	62.5	16	30	152
Adenocarcinoma (Liver cancer)	Liver cancer	0.0001	29	74.3	39	97	207
Bone marrow (Leukemia)	Leukemia	0.0001	12	42.8	28	23	141
Lymphocytes (Leukemia)	Leukemia	0.0001	26	92.8	28	91	141
Acute lymphocytic leukemia - relapse (Leukemia)	Leukemia	0.0002	6	21.4	28	7	141
Acute lymphocytic leukemia (Leukemia)	Leukemia	0.0002	27	93.1	29	99	149

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
vision	4.2e-90	50	100	50	100	4566
perception of light	3.1e-89	50	100	50	103	4566
response to light	2.1e-65	50	100	50	256	4566
response to radiation	9.4e-65	50	100	50	263	4566
response to abiotic stimulus	1.4e-29	50	100	50	1228	4566
phototransduction	1.6e-14	10	20	50	24	4566
rhodopsin mediated phototransduction	7.3e-11	7	14	50	15	4566
rhodopsin mediated signaling	2.0e-09	6	12	50	13	4566
structural constituent of eye lens	2.5e-06	4	8	50	10	4566
rhodopsin-like receptor activity	2.9e-06	10	20	50	147	4566
G-protein signaling\, coupled to IP3 second messenger (phospholipase C activating)	1.0e-05	6	12	50	48	4566
G-protein coupled receptor activity	1.1e-05	10	20	50	170	4566
G-protein coupled photoreceptor activity	1.2e-05	3	6	50	5	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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