Module 415

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:	11
Num genes:	13 (see 448 additional genes for this module)
Num experiments:	129 (66 induced, 63 repressed)
Parent module:	None
Children modules:	316 328

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.
anticoagulant activity
nucleotide receptor activity
GPI_anchored membrane_bound receptor
nicotinic acetylcholine_activated cation_selective channel activity
nicotinic acetylcholine_gated receptor_channel complex
acetylcholine receptor activity
excitatory extracellular ligand_gated ion channel activity
ion channel activity
alpha_type channel activity
ion transport
small molecule transport

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*	3.9e-54	58	87.8	66	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.3e-52	58	87.8	66	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.7e-33	43	65.1	66	156	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	8.4e-16	31	49.2	63	197	1945
Cancer and cell line (Liver cancer)	Liver cancer	4.7e-10	38	100	38	126	207
Liver cancer cell line (Liver cancer)	Liver cancer	1.4e-08	10	26.3	38	10	207
Liver tissue (Liver cancer*)	Liver cancer*	1.1e-07	21	33.3	63	187	1945
Cell line (Liver cancer)	Liver cancer	1.4e-07	10	26.3	38	11	207
Non-tumor liver tissue (Liver cancer)	Liver cancer	3.1e-06	36	62.0	58	76	207
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.8e-05	16	25.3	63	156	1945
Metastasis (Liver cancer)	Liver cancer	0.0003	7	18.4	38	10	207

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
small molecule transport	2.1e-16	11	84.6	13	121	4566
alpha-type channel activity	2.2e-08	7	53.8	13	133	4566
response to drug	7.1e-08	7	53.8	13	157	4566
porter activity	8.9e-08	5	38.4	13	45	4566
obsolete	2.3e-06	11	84.6	13	990	4566
organic acid transporter activity	3.7e-06	4	30.7	13	41	4566
response to chemical substance	7.1e-06	7	53.8	13	308	4566
ion channel activity	1.1e-05	5	38.4	13	117	4566
channel/pore class transporter activity	1.7e-05	7	53.8	13	351	4566
proton-dependent oligopeptide transporter activity	7.0e-05	3	23.0	13	30	4566
carboxylic acid transporter activity	7.7e-05	3	23.0	13	31	4566
peptide transporter activity	7.7e-05	3	23.0	13	31	4566
symporter activity	7.7e-05	3	23.0	13	31	4566
extracellular ligand-gated ion channel activity	9.3e-05	3	23.0	13	33	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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