Module 93 -- Oxidoreductases

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:	182 (see 2280 additional genes for this module)
Num experiments:	547 (227 induced, 320 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.
oxidoreductase activity
electron transporter 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*	2.2e-64	110	48.4	227	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	5.5e-61	110	48.4	227	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.2e-46	87	38.3	227	156	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	2.8e-23	102	31.8	320	252	1945
Cancer (Lung cancer*)	Lung cancer*	2.8e-23	102	31.8	320	252	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	1.0e-22	107	33.4	320	276	1945
Lung cancer (Lung cancer*)	Lung cancer*	2.7e-17	89	27.8	320	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	2.7e-17	89	27.8	320	238	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	1.5e-15	67	60.9	110	76	207
Cancer and cell line (Liver cancer)	Liver cancer	1.7e-15	64	96.9	66	126	207
Prostate (Prostate cancer*)	Prostate cancer*	5.5e-14	48	15	320	101	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	3.0e-12	72	22.5	320	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	3.0e-12	72	22.5	320	205	1945
Cancer (Liver cancer)	Liver cancer	9.6e-08	54	81.8	66	115	207
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	5.4e-06	56	17.5	320	197	1945
Liver cancer cell line (Liver cancer)	Liver cancer	6.6e-06	10	15.1	66	10	207
Metastasis (Liver cancer)	Liver cancer	6.6e-06	10	15.1	66	10	207
Adenocarcinoma (Liver cancer)	Liver cancer	2.2e-05	45	68.1	66	97	207
Hematologic samples and cell lines (Various tumors)	Various tumors	2.6e-05	16	57.1	28	37	154
Hematologic samples (Various tumors)	Various tumors	2.6e-05	16	57.1	28	37	154
CNS cancer or cell line (Various tumors)	Various tumors	3.2e-05	10	35.7	28	16	154
CNS tumor (Various tumors)	Various tumors	3.2e-05	10	35.7	28	16	154
Prostate (Various tumors)	Various tumors	4.1e-05	6	50	12	12	154
Cell line (Liver cancer)	Liver cancer	5.3e-05	10	15.1	66	11	207
Normal tissue (Liver cancer)	Liver cancer	9.4e-05	14	12.7	110	14	207
Centroblasts (Various tumors)	Various tumors	0.0001	5	17.8	28	5	154
GC B like DLBCL (Various tumors)	Various tumors	0.0001	5	17.8	28	5	154
Invasive liver tumor (Liver cancer)	Liver cancer	0.0002	22	33.3	66	38	207
Hematologic samples (B lymphoma)	B lymphoma	0.0002	7	38.8	18	22	245
Adenocarcinoma - extrapulmonary metastasis (Lung cancer)	Lung cancer	0.0003	12	11.2	107	14	276
Hepatitis infected liver (Liver cancer*)	Liver cancer*	0.0003	42	13.1	320	156	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
electron transporter activity	1.6e-207	165	90.6	182	269	4566
oxidoreductase activity	1.4e-203	161	88.4	182	254	4566
electron transport	1.5e-82	78	42.8	182	128	4566
photosynthesis\, light reaction	1.5e-71	69	37.9	182	115	4566
photosynthesis	1.1e-63	73	40.1	182	162	4566
energy pathways	1.8e-62	78	42.8	182	200	4566
oxidoreductase activity\, acting on CH-OH group of donors	6.8e-31	31	17.0	182	53	4566
oxidoreductase activity\, acting on the CH-OH group of donors\, NAD or NADP as acceptor	6.8e-31	31	17.0	182	53	4566
mitochondrion	2.5e-26	49	26.9	182	207	4566
oxidoreductase activity\, acting on paired donors\, with incorporation or reduction of molecular oxygen	3.7e-26	26	14.2	182	44	4566
carboxylic acid metabolism	5.0e-25	40	21.9	182	138	4566
organic acid metabolism	8.2e-24	39	21.4	182	139	4566
catalytic activity	2.5e-20	127	69.7	182	1677	4566
monovalent inorganic cation transporter activity	4.0e-20	28	15.3	182	80	4566
oxidoreductase activity\, acting on the aldehyde or oxo group of donors	8.6e-16	13	7.1	182	17	4566
oxidoreductase activity\, acting on the CH-CH group of donors	8.6e-16	13	7.1	182	17	4566
NADH dehydrogenase (ubiquinone) activity	3.0e-15	15	8.2	182	26	4566
microsome	3.9e-15	21	11.5	182	61	4566
aldehyde metabolism	7.9e-15	10	5.4	182	10	4566
fatty acid metabolism	1.2e-14	20	10.9	182	57	4566
NADH dehydrogenase activity	4.7e-14	14	7.6	182	25	4566
oxidative phosphorylation	5.8e-14	12	6.5	182	17	4566
ion transporter activity	1.2e-13	29	15.9	182	144	4566
monooxygenase activity	3.3e-13	13	7.1	182	23	4566
peroxidase activity	3.5e-13	11	6.0	182	15	4566
alcohol dehydrogenase activity	4.8e-13	10	5.4	182	12	4566
response to xenobiotic stimulus	7.7e-13	27	14.8	182	133	4566
oxidoreductase activity\, acting on the aldehyde or oxo group of donors\, NAD or NADP as acceptor	6.9e-12	10	5.4	182	14	4566
plasmodesma	7.1e-12	24	13.1	182	114	4566
mitochondrial membrane	9.9e-12	17	9.3	182	54	4566
ATP synthesis coupled electron transport (sensu Eukarya)	2.0e-11	10	5.4	182	15	4566
cytochrome P450 activity	2.0e-11	10	5.4	182	15	4566
oxidoreductase activity\, acting on single donors with incorporation of molecular oxygen	5.1e-11	10	5.4	182	16	4566
protein-disulfide reduction	5.1e-11	10	5.4	182	16	4566
lipid metabolism	1.8e-10	25	13.7	182	143	4566
alcohol dehydrogenase activity\, zinc-dependent	2.3e-10	8	4.3	182	10	4566
aldehyde dehydrogenase activity	2.3e-10	8	4.3	182	10	4566
oxidoreductase activity\, acting on the CH-CH group of donors\, other acceptors	2.3e-10	8	4.3	182	10	4566
inner membrane	3.2e-10	12	6.5	182	29	4566
mitochondrial electron transport\, NADH to ubiquinone	3.5e-10	9	4.9	182	14	4566
sodium ion transporter activity	3.8e-10	15	8.2	182	50	4566
endoplasmic reticulum	6.2e-10	25	13.7	182	151	4566
metal ion transporter activity	6.7e-10	16	8.7	182	60	4566
cbb3-type cytochrome c oxidase	2.3e-09	8	4.3	182	12	4566
glutathione peroxidase activity	3.7e-09	6	3.2	182	6	4566
mitochondrial electron transport chain	4.8e-09	7	3.8	182	9	4566
cytochrome c oxidase activity	5.9e-09	8	4.3	182	13	4566
cation transporter activity	9.9e-09	13	7.1	182	45	4566
alcohol metabolism	1.3e-08	8	4.3	182	14	4566
fatty acid biosynthesis	1.5e-08	10	5.4	182	25	4566
membrane fraction	1.9e-08	34	18.6	182	304	4566
organic acid biosynthesis	2.6e-08	11	6.0	182	33	4566
carboxylic acid biosynthesis	3.8e-08	11	6.0	182	34	4566
hydrogen ion transporter activity	4.0e-08	13	7.1	182	50	4566
response to chemical substance	9.2e-08	33	18.1	182	308	4566
ubiquinol-cytochrome c reductase activity	9.5e-08	5	2.7	182	5	4566
disulfide oxidoreductase activity	9.5e-08	7	3.8	182	12	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	2.8e-07	6	3.2	182	9	4566
oxidoreductase activity\, acting on the CH-NH2 group of donors	2.8e-07	6	3.2	182	9	4566
oxidoreductase activity\, acting on the CH-NH group of donors	2.8e-07	6	3.2	182	9	4566
eicosanoid metabolism	2.8e-07	8	4.3	182	19	4566
acyl-CoA dehydrogenase activity	5.5e-07	5	2.7	182	6	4566
lipid biosynthesis	1.0e-06	10	5.4	182	37	4566
peroxisome	1.4e-06	9	4.9	182	30	4566
oxidoreductase activity\, acting on the CH-NH group of donors\, NAD or NADP as acceptor	1.8e-06	5	2.7	182	7	4566
amine metabolism	1.9e-06	9	4.9	182	31	4566
oxygen and reactive oxygen species metabolism	1.9e-06	7	3.8	182	17	4566
response to oxidative stress	1.9e-06	7	3.8	182	17	4566
eicosanoid biosynthesis	3.1e-06	7	3.8	182	18	4566
amino acid and derivative metabolism	4.6e-06	8	4.3	182	26	4566
oxidoreductase activity\, acting on NADH or NADPH	4.8e-06	5	2.7	182	8	4566
oxidoreductase activity\, acting on the CH-NH2 group of donors\, oxygen as acceptor	4.8e-06	5	2.7	182	8	4566
outer membrane	8.4e-06	6	3.2	182	14	4566
xenobiotic metabolism	9.8e-06	9	4.9	182	37	4566
amine oxidase activity	1.1e-05	4	2.1	182	5	4566
tricarboxylic acid cycle	1.3e-05	6	3.2	182	15	4566
sulfur metabolism	1.5e-05	22	12.0	182	205	4566
mitochondrial matrix	2.0e-05	7	3.8	182	23	4566
fatty acid beta-oxidation	2.0e-05	5	2.7	182	10	4566
fatty acid oxidation	2.0e-05	5	2.7	182	10	4566
oxidoreductase activity\, acting on paired donors\, with incorporation or reduction of molecular oxygen\, 2-oxoglutarate as one donor\, and incorporation of one atom each of oxygen into both donors	3.4e-05	4	2.1	182	6	4566
protein disulfide oxidoreductase activity	3.4e-05	4	2.1	182	6	4566
superoxide metabolism	3.4e-05	4	2.1	182	6	4566
aromatic compound metabolism	3.7e-05	7	3.8	182	25	4566
steroid metabolism	4.9e-05	7	3.8	182	26	4566
transition metal ion binding	5.3e-05	18	9.8	182	160	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 547 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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