Module 367

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:	3
Num genes:	29 (see 1237 additional genes for this module)
Num experiments:	106 (50 induced, 56 repressed)
Parent module:	None
Children modules:	251

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.
rhodopsin mediated signaling
rhodopsin mediated phototransduction
G_protein signaling, coupled to IP3 second messenger (phospholipase C activating)

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
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.8e-09	19	38	50	156	1945
Liver tissue (Liver cancer*)	Liver cancer*	4.1e-08	19	38	50	187	1945
Liver tissue (Liver cancer*)	Liver cancer*	6.0e-08	20	35.7	56	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	9.8e-08	19	38	50	197	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.4e-07	20	35.7	56	197	1945
Activated B like DLBCL (B lymphoma)	B lymphoma	2.5e-06	8	72.7	11	30	245
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	2.6e-06	11	64.7	17	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	2.6e-06	11	64.7	17	30	182
Hepatitis infected liver (Liver cancer*)	Liver cancer*	3.4e-06	16	28.5	56	156	1945
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	5.7e-06	17	30.3	56	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	5.7e-06	17	30.3	56	182	1945
Live bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0001	4	33.3	12	5	148
Stimulated immune cells (Stimulated PBMC*)	Stimulated PBMC*	0.0001	13	23.2	56	143	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
G-protein signaling\, coupled to IP3 second messenger (phospholipase C activating)	1.6e-55	27	93.1	29	48	4566
rhodopsin-like receptor activity	3.7e-26	21	72.4	29	147	4566
G-protein coupled receptor activity	9.3e-25	21	72.4	29	170	4566
cytosolic calcium ion concentration elevation	7.9e-22	12	41.3	29	24	4566
G-protein coupled receptor protein signaling pathway	2.6e-21	21	72.4	29	245	4566
rhodopsin mediated signaling	5.2e-21	10	34.4	29	13	4566
rhodopsin mediated phototransduction	5.4e-20	10	34.4	29	15	4566
cell surface receptor linked signal transduction	3.6e-19	20	68.9	29	259	4566
peptide receptor activity	1.4e-18	13	44.8	29	55	4566
peptide receptor activity\, G-protein coupled	3.1e-18	13	44.8	29	58	4566
phototransduction	3.4e-17	10	34.4	29	24	4566
transmembrane receptor activity	8.8e-16	21	72.4	29	448	4566
receptor activity	9.5e-15	22	75.8	29	582	4566
signal transducer activity	4.4e-13	25	86.2	29	1026	4566
integral to plasma membrane	5.1e-13	21	72.4	29	612	4566
sensory perception	7.6e-12	21	72.4	29	700	4566
phosphatidylinositol-4\,5-bisphosphate hydrolysis	7.8e-12	6	20.6	29	10	4566
response to light	7.7e-11	14	48.2	29	256	4566
response to radiation	1.1e-10	14	48.2	29	263	4566
signal transduction	2.2e-10	21	72.4	29	831	4566
vision	2.2e-10	10	34.4	29	100	4566
perception of light	3.0e-10	10	34.4	29	103	4566
thermoregulation	3.7e-10	10	34.4	29	105	4566
response to abiotic stimulus	4.7e-10	24	82.7	29	1228	4566
inflammatory response	4.9e-10	10	34.4	29	108	4566
conjugation without cellular fusion	8.0e-10	11	37.9	29	152	4566
cell communication	1.4e-08	21	72.4	29	1030	4566
invasive growth	2.0e-08	5	17.2	29	15	4566
cellular morphogenesis	7.8e-08	5	17.2	29	19	4566
protein kinase C activation	9.0e-08	4	13.7	29	8	4566
chemotaxis	2.3e-07	7	24.1	29	73	4566
energy taxis	2.5e-07	7	24.1	29	74	4566
phospholipase C activation	2.6e-07	4	13.7	29	10	4566
taxis	3.1e-07	7	24.1	29	76	4566
chemokine binding	4.2e-07	4	13.7	29	11	4566
G-protein chemoattractant receptor activity	1.2e-06	4	13.7	29	14	4566
circulation	2.1e-05	5	17.2	29	56	4566
nucleotide receptor activity	9.9e-05	3	10.3	29	15	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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