Module 212 -- Catalytic activities/metabolism

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:	4
Num genes:	329 (see 1353 additional genes for this module)
Num experiments:	697 (312 induced, 385 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.
Chen02 47
catalytic activity
carbohydrate metabolism
Whitfield02 9

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*	2.4e-56	119	38.1	312	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.1e-52	119	38.1	312	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.4e-41	95	30.4	312	156	1945
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	1.6e-33	30	96.7	31	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	1.6e-33	30	96.7	31	30	182
Non-tumor liver tissue (Liver cancer)	Liver cancer	2.9e-17	71	59.6	119	76	207
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	4.9e-16	34	57.6	59	46	245
Leukemia (B lymphoma)	B lymphoma	4.9e-16	34	57.6	59	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	4.9e-16	34	57.6	59	46	245
Cancer and cell line (Liver cancer)	Liver cancer	3.9e-14	74	91.3	81	126	207
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	3.6e-10	28	8.9	312	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	3.6e-10	28	8.9	312	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	3.6e-10	28	8.9	312	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	3.6e-10	28	8.9	312	53	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.1e-08	71	18.4	384	197	1945
Cancer (Liver cancer)	Liver cancer	2.9e-08	64	79.0	81	115	207
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	3.5e-06	20	90.9	22	67	144
Hepatitis infected liver (Liver cancer*)	Liver cancer*	3.7e-06	54	14.0	384	156	1945
Adenocarcinoma (Liver cancer)	Liver cancer	3.9e-06	54	66.6	81	97	207
Liver tissue (Liver cancer*)	Liver cancer*	7.7e-06	61	15.8	384	187	1945
Cell line (B lymphoma)	B lymphoma	2.3e-05	9	23.6	38	14	245
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	2.7e-05	36	94.7	38	167	245
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	3.7e-05	32	84.2	38	134	245
Small cell lung cancer (Lung cancer)	Lung cancer	4.3e-05	9	12	75	10	276
B. petrussis 537 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	5.4e-05	5	22.7	22	5	144
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	5.4e-05	5	22.7	22	5	144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	5.4e-05	5	22.7	22	5	144
Liver cancer cell line (Liver cancer)	Liver cancer	5.8e-05	10	12.3	81	10	207
Metastasis (Liver cancer)	Liver cancer	5.8e-05	10	12.3	81	10	207
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	9.2e-05	20	90.9	22	78	144
Hepatocellular carcinoma (Liver cancer)	Liver cancer	0.0001	54	66.6	81	104	207
Invasive liver tumor (Liver cancer)	Liver cancer	0.0002	25	30.8	81	38	207
Bone marrow (Leukemia)	Leukemia	0.0002	6	75	8	23	141
Hematologic samples (B lymphoma)	B lymphoma	0.0002	13	22.0	59	22	245
Normal tissue (Liver cancer)	Liver cancer	0.0003	14	11.7	119	14	207
Activated B like DLBCL (B lymphoma)	B lymphoma	0.0004	12	31.5	38	30	245
Cell line (Liver cancer)	Liver cancer	0.0004	10	12.3	81	11	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
catalytic activity	3.7e-83	250	90.5	276	1677	4566
oxidoreductase activity	1.9e-27	67	24.2	276	254	4566
electron transporter activity	6.7e-22	62	22.4	276	269	4566
carboxylic acid metabolism	9.6e-20	42	15.2	276	138	4566
organic acid metabolism	1.0e-18	41	14.8	276	139	4566
response to xenobiotic stimulus	3.3e-15	36	13.0	276	133	4566
regulation of metabolism	1.0e-13	60	21.7	276	365	4566
energy pathways	2.1e-13	42	15.2	276	200	4566
hydrolase activity	1.4e-12	94	34.0	276	783	4566
response to chemical substance	1.0e-10	49	17.7	276	308	4566
photosynthesis\, light reaction	4.2e-10	27	9.7	276	115	4566
photosynthesis	1.0e-09	32	11.5	276	162	4566
microsome	1.1e-09	19	6.8	276	61	4566
electron transport	1.1e-09	28	10.1	276	128	4566
amino acid metabolism	8.2e-09	28	10.1	276	139	4566
oxidoreductase activity\, acting on paired donors\, with incorporation or reduction of molecular oxygen	1.6e-08	15	5.4	276	44	4566
fatty acid metabolism	1.8e-08	17	6.1	276	57	4566
carbohydrate metabolism	4.5e-08	25	9.0	276	123	4566
lyase activity	6.3e-08	19	6.8	276	76	4566
aromatic compound metabolism	6.7e-08	11	3.9	276	25	4566
phenylalanine metabolism	8.8e-08	7	2.5	276	9	4566
amine metabolism	9.4e-08	12	4.3	276	31	4566
peptidase activity	9.5e-08	32	11.5	276	193	4566
amino acid and derivative metabolism	1.1e-07	11	3.9	276	26	4566
response to toxin	1.1e-07	11	3.9	276	26	4566
catabolism	3.9e-07	33	11.9	276	215	4566
sulfur metabolism	4.0e-07	32	11.5	276	205	4566
aromatic amino acid family metabolism	1.1e-06	6	2.1	276	8	4566
phenylalanine catabolism	1.1e-06	6	2.1	276	8	4566
oxidoreductase activity\, acting on CH-OH group of donors	1.7e-06	14	5.0	276	53	4566
oxidoreductase activity\, acting on the CH-OH group of donors\, NAD or NADP as acceptor	1.7e-06	14	5.0	276	53	4566
energy derivation by oxidation of organic compounds	2.2e-06	14	5.0	276	54	4566
oxidoreductase activity\, acting on the CH-CH group of donors	2.4e-06	8	2.8	276	17	4566
isomerase activity	4.0e-06	12	4.3	276	42	4566
transferase activity\, transferring acyl groups	5.3e-06	12	4.3	276	43	4566
carboxylic ester hydrolase activity	1.1e-05	9	3.2	276	26	4566
endopeptidase activity	1.9e-05	18	6.5	276	99	4566
transferase activity\, transferring groups other than amino-acyl groups	2.5e-05	11	3.9	276	42	4566
carbon-oxygen lyase activity	2.6e-05	10	3.6	276	35	4566
glutathione transferase activity	3.1e-05	6	2.1	276	12	4566
hydro-lyase activity	3.2e-05	9	3.2	276	29	4566
monooxygenase activity	3.5e-05	8	2.8	276	23	4566
proteolysis and peptidolysis	4.3e-05	25	9.0	276	176	4566
serine-type endopeptidase activity	4.7e-05	14	5.0	276	69	4566
toxin metabolism	4.8e-05	7	2.5	276	18	4566
serine-type peptidase activity	6.6e-05	15	5.4	276	80	4566
oxidoreductase activity\, acting on paired donors\, with incorporation or reduction of molecular oxygen\, reduced flavin or flavoprotein as one donor\, and incorporation of one atom of oxygen	8.0e-05	5	1.8	276	9	4566
transaminase activity	9.1e-05	6	2.1	276	14	4566
lipid metabolism	0.0001	21	7.6	276	143	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.

Note: Since there are 697 experiments, this image does not display the individual experiment names, but rather condenses each experiment to a single pixel without displaying its name. You can fully view the image for this module within GeneXPress, by loading any of the four files mentioned in the line above

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