Module 109 -- Serine proteases

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:	40 (see 2095 additional genes for this module)
Num experiments:	276 (93 induced, 183 repressed)
Parent module:	None
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.
trypsin activity
chymotrypsin activity

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*	5.0e-49	65	69.8	93	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	2.6e-47	65	69.8	93	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.0e-28	46	49.4	93	156	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	1.0e-19	53	81.5	65	76	207
Cancer and cell line (Lung cancer*)	Lung cancer*	2.9e-14	61	33.3	183	252	1945
Cancer (Lung cancer*)	Lung cancer*	2.9e-14	61	33.3	183	252	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	7.4e-13	62	33.8	183	276	1945
Lung cancer (Lung cancer*)	Lung cancer*	7.3e-12	55	30.0	183	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	7.3e-12	55	30.0	183	238	1945
Cancer and cell line (Liver cancer)	Liver cancer	1.7e-11	43	100	43	126	207
B cells (Leukemia)	Leukemia	1.1e-09	22	100	22	62	141
Lung carcinoid (Lung cancer)	Lung cancer	1.8e-08	16	25.8	62	20	276
Normal tissue (Liver cancer)	Liver cancer	3.1e-08	14	21.5	65	14	207
Liver cancer cell line (Liver cancer)	Liver cancer	6.0e-08	10	23.2	43	10	207
Cell line (Breast cancer)	Breast cancer	2.5e-07	13	72.2	18	30	152
Cell line (Liver cancer)	Liver cancer	5.6e-07	10	23.2	43	11	207
Metastasis (Liver cancer)	Liver cancer	2.9e-06	9	20.9	43	10	207
Bone marrow (Leukemia)	Leukemia	4.7e-06	12	54.5	22	23	141
Acute lymphocytic leukemia (Leukemia)	Leukemia	1.1e-05	25	100	25	99	149
Lymphocytes (Leukemia)	Leukemia	2.3e-05	22	100	22	91	141
Invasive liver tumor (Liver cancer)	Liver cancer	3.4e-05	18	41.8	43	38	207
Breast cancer cell line (Breast cancer)	Breast cancer	0.0001	8	44.4	18	17	152
Primary blood mononuclear cells (Leukemia)	Leukemia	0.0001	10	45.4	22	21	141
Centroblasts (Various tumors)	Various tumors	0.0001	5	17.2	29	5	154
GC B like DLBCL (Various tumors)	Various tumors	0.0001	5	17.2	29	5	154
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	0.0001	34	18.5	183	197	1945
Female hormonal cancer cell line (Breast cancer)	Breast cancer	0.0003	7	38.8	18	15	152

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
trypsin activity	4.1e-89	40	100	40	50	4566
chymotrypsin activity	3.0e-86	39	97.5	40	48	4566
serine-type endopeptidase activity	9.5e-80	40	100	40	69	4566
serine-type peptidase activity	4.3e-76	40	100	40	80	4566
endopeptidase activity	3.3e-71	40	100	40	99	4566
regulation of catabolism	6.1e-61	40	100	40	162	4566
proteolysis and peptidolysis	2.6e-59	40	100	40	176	4566
peptidase activity	1.6e-57	40	100	40	193	4566
catabolism	2.0e-55	40	100	40	215	4566
regulation of metabolism	1.6e-45	40	100	40	365	4566
hydrolase activity	1.0e-31	40	100	40	783	4566
catalytic activity	2.9e-18	40	100	40	1677	4566
blood coagulation factor activity	6.2e-11	6	15	40	10	4566
blood coagulation	1.5e-10	9	22.5	40	48	4566
hemostasis	2.2e-10	9	22.5	40	50	4566
defense/immunity protein activity	6.0e-10	11	27.5	40	103	4566
complement activity	3.1e-07	5	12.5	40	18	4566
regulation of complement activation	1.8e-06	5	12.5	40	25	4566
complement activation	2.2e-06	5	12.5	40	26	4566
cytolysis	8.5e-06	4	10	40	16	4566
complement activation\, classical pathway	3.2e-05	4	10	40	22	4566
scavenger receptor activity	5.0e-05	3	7.5	40	9	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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