Module 10

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:	21 (see 2235 additional genes for this module)
Num experiments:	311 (155 induced, 156 repressed)
Parent module:	58
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.
regulation of complement activation
complement activation

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 (General compendium)	General compendium	2.7e-37	72	46.4	155	187	1946
Liver tissue, cancer or cell line (General compendium)	General compendium	1.8e-35	72	46.4	155	197	1946
Lung cancer (General compendium)	General compendium	9.3e-24	67	42.9	156	244	1946
Lung tissue, cancer or cell line (General compendium)	General compendium	5.0e-23	74	47.4	156	304	1946
Hepatitis infected liver (General compendium)	General compendium	2.2e-22	52	33.5	155	156	1946
Lung cancer or cell line (General compendium)	General compendium	9.0e-22	67	42.9	156	262	1946
Cancer and cell line (General compendium)	General compendium	6.9e-21	155	99.3	156	1429	1946
Cancer (General compendium)	General compendium	1.9e-11	127	81.4	156	1110	1946
Lung carcinoid (Lung cancer)	Lung cancer	3.2e-11	19	25.6	74	20	276
Cancer and cell line (Liver cancer)	Liver cancer	3.3e-11	42	100	42	126	207
Non-tumor liver tissue (Liver cancer)	Liver cancer	9.0e-11	48	66.6	72	76	207
Non small cell lung cancer (General compendium)	General compendium	3.0e-10	43	27.5	156	205	1946
Non small cell lung cancer and cell line (General compendium)	General compendium	5.2e-09	43	27.5	156	223	1946
Liver cancer cell line (Liver cancer)	Liver cancer	4.6e-08	10	23.8	42	10	207
Cell line (Liver cancer)	Liver cancer	4.3e-07	10	23.8	42	11	207
Cell line (Breast cancer)	Breast cancer	1.3e-06	12	70.5	17	30	152
Metastasis (Liver cancer)	Liver cancer	2.3e-06	9	21.4	42	10	207
Normal tissue (Liver cancer)	Liver cancer	5.0e-06	13	18.0	72	14	207
Liver tissue, cancer or cell line (General compendium)	General compendium	1.3e-05	33	21.1	156	197	1946
Adenocarcinoma (General compendium)	General compendium	2.9e-05	59	38.0	155	466	1946
Pancreatic cancer (Various tumors)	Various tumors	0.0001	5	31.2	16	7	154
Adenocarcinoma (General compendium)	General compendium	0.0001	57	36.5	156	466	1946
Squamous cell lung cancer (Lung cancer)	Lung cancer	0.0002	19	25.6	74	35	276
Colon cancer (Liver cancer)	Liver cancer	0.0002	5	11.9	42	5	207
Colon cancer metastasis to liver (Liver cancer)	Liver cancer	0.0002	5	11.9	42	5	207
Colon cancer or cell line (Liver cancer)	Liver cancer	0.0002	5	11.9	42	5	207
Colon tissue, cancer or cell line (Liver cancer)	Liver cancer	0.0002	5	11.9	42	5	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
complement activation	4.0e-53	21	100	21	26	4609
regulation of complement activation	1.5e-49	20	95.2	21	25	4609
complement activation\, classical pathway	7.2e-44	18	85.7	21	22	4609
humoral immune response	7.1e-35	21	100	21	119	4609
complement activity	1.6e-32	14	66.6	21	18	4609
response to pest/pathogen/parasite	1.0e-31	21	100	21	164	4609
immune response	1.0e-21	21	100	21	471	4609
response to biotic stimulus	2.0e-19	21	100	21	602	4609
defense/immunity protein activity	3.2e-19	14	66.6	21	103	4609
response to stress	7.7e-17	21	100	21	796	4609
complement activation\, alternative pathway	1.5e-15	7	33.3	21	10	4609
cytolysis	4.9e-09	5	23.8	21	16	4609
response to pathogenic bacteria	6.5e-08	4	19.0	21	10	4609
extracellular space	1.4e-07	9	42.8	21	212	4609
chymotrypsin activity	1.9e-06	5	23.8	21	49	4609
trypsin activity	2.4e-06	5	23.8	21	51	4609
serine-type endopeptidase activity	1.1e-05	5	23.8	21	70	4609
cell death	2.0e-05	6	28.5	21	134	4609
serine-type peptidase activity	2.4e-05	5	23.8	21	81	4609
endopeptidase activity	6.7e-05	5	23.8	21	100	4609

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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