Module 43 -- Energy pathways

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:	99 (see 1623 additional genes for this module)
Num experiments:	299 (158 induced, 141 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.
energy pathways
photosynthesis, light reaction
electron transport
photosynthesis

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*	2.9e-60	91	57.9	157	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.2e-57	91	57.9	157	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	4.8e-41	70	44.5	157	156	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	5.5e-21	54	38.2	141	197	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	9.7e-20	64	70.3	91	76	207
Cancer and cell line (Liver cancer)	Liver cancer	2.0e-16	63	98.4	64	126	207
Prostate (Prostate cancer*)	Prostate cancer*	4.8e-15	33	23.4	141	101	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	3.9e-14	40	28.3	141	156	1945
Liver tissue (Liver cancer*)	Liver cancer*	4.4e-14	44	31.2	141	187	1945
Cancer (Liver cancer)	Liver cancer	5.8e-08	53	82.8	64	115	207
Liver cancer cell line (Liver cancer)	Liver cancer	4.7e-06	10	15.6	64	10	207
Metastasis (Liver cancer)	Liver cancer	4.7e-06	10	15.6	64	10	207
Adenocarcinoma (Liver cancer)	Liver cancer	5.2e-06	45	70.3	64	97	207
Cell line (Liver cancer)	Liver cancer	3.9e-05	10	15.6	64	11	207
Lung carcinoid (Lung cancer)	Lung cancer	4.6e-05	6	50	12	20	276
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	5.9e-05	13	9.2	141	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	5.9e-05	13	9.2	141	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	5.9e-05	13	9.2	141	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	5.9e-05	13	9.2	141	53	1945
Normal tissue (Liver cancer)	Liver cancer	0.0001	13	14.2	91	14	207
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	0.0001	13	8.2	157	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	0.0001	13	8.2	157	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	0.0001	13	8.2	157	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	0.0001	13	8.2	157	53	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
energy pathways	1.1e-131	94	94.9	99	200	4566
photosynthesis	1.4e-95	75	75.7	99	162	4566
electron transport	1.2e-81	64	64.6	99	128	4566
photosynthesis\, light reaction	4.1e-73	58	58.5	99	115	4566
electron transporter activity	3.2e-58	65	65.6	99	269	4566
oxidoreductase activity	3.9e-52	60	60.6	99	254	4566
mitochondrion	6.0e-28	39	39.3	99	207	4566
energy derivation by oxidation of organic compounds	9.6e-24	22	22.2	99	54	4566
main pathways of carbohydrate metabolism	8.4e-17	15	15.1	99	35	4566
mitochondrial membrane	7.4e-15	16	16.1	99	54	4566
monovalent inorganic cation transporter activity	2.7e-14	18	18.1	99	80	4566
oxidoreductase activity\, acting on paired donors\, with incorporation or reduction of molecular oxygen	1.3e-13	14	14.1	99	44	4566
monooxygenase activity	3.0e-13	11	11.1	99	23	4566
tricarboxylic acid cycle	3.2e-12	9	9.0	99	15	4566
carbohydrate metabolism	6.5e-12	19	19.1	99	123	4566
fatty acid metabolism	7.1e-12	14	14.1	99	57	4566
oxidoreductase activity\, acting on the CH-CH group of donors	1.5e-11	9	9.0	99	17	4566
ion transporter activity	1.1e-10	19	19.1	99	144	4566
oxidoreductase activity\, acting on the CH-CH group of donors\, other acceptors	2.0e-10	7	7.0	99	10	4566
cytochrome P450 activity	2.0e-10	8	8.0	99	15	4566
microsome	2.9e-10	13	13.1	99	61	4566
inner membrane	5.1e-09	9	9.0	99	29	4566
mitochondrial electron transport\, NADH to ubiquinone	5.5e-09	7	7.0	99	14	4566
mitochondrial inner membrane	9.3e-09	10	10.1	99	41	4566
ATP synthesis coupled electron transport (sensu Eukarya)	1.0e-08	7	7.0	99	15	4566
plasmodesma	1.3e-08	15	15.1	99	114	4566
membrane fraction	1.4e-08	24	24.2	99	304	4566
fatty acid beta-oxidation	1.7e-08	6	6.0	99	10	4566
fatty acid oxidation	1.7e-08	6	6.0	99	10	4566
protein-disulfide reduction	1.7e-08	7	7.0	99	16	4566
acyl-CoA dehydrogenase activity	2.5e-08	5	5.0	99	6	4566
carboxylic acid metabolism	2.7e-08	16	16.1	99	138	4566
NADH dehydrogenase activity	2.9e-08	8	8.0	99	25	4566
oxidative phosphorylation	2.9e-08	7	7.0	99	17	4566
organic acid metabolism	3.0e-08	16	16.1	99	139	4566
NADH dehydrogenase (ubiquinone) activity	4.1e-08	8	8.0	99	26	4566
hydrogen ion transporter activity	7.2e-08	10	10.1	99	50	4566
sodium ion transporter activity	7.2e-08	10	10.1	99	50	4566
cbb3-type cytochrome c oxidase	7.4e-08	6	6.0	99	12	4566
endoplasmic reticulum	9.8e-08	16	16.1	99	151	4566
catalytic activity	1.1e-07	62	62.6	99	1677	4566
cytochrome c oxidase activity	1.3e-07	6	6.0	99	13	4566
energy reserve metabolism	1.3e-07	6	6.0	99	13	4566
peroxisome	1.4e-07	8	8.0	99	30	4566
glycolysis	1.6e-07	7	7.0	99	21	4566
metal ion transporter activity	4.4e-07	10	10.1	99	60	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	5.0e-07	5	5.0	99	9	4566
cation transporter activity	4.0e-06	8	8.0	99	45	4566
glycogen metabolism	1.3e-05	4	4.0	99	8	4566
oxidoreductase activity\, acting on CH-OH group of donors	1.4e-05	8	8.0	99	53	4566
oxidoreductase activity\, acting on the CH-OH group of donors\, NAD or NADP as acceptor	1.4e-05	8	8.0	99	53	4566
mitochondrial electron transport chain	2.4e-05	4	4.0	99	9	4566
hydro-lyase activity	2.8e-05	6	6.0	99	29	4566
lyase activity	3.1e-05	9	9.0	99	76	4566
synaptic junction	3.1e-05	14	14.1	99	183	4566
regulation of metabolism	7.9e-05	20	20.2	99	365	4566
carbon-oxygen lyase activity	8.7e-05	6	6.0	99	35	4566
isocitrate dehydrogenase activity	9.5e-05	3	3.0	99	5	4566
oxidoreductase activity\, acting on the CH-CH group of donors\, oxygen as acceptor	9.5e-05	3	3.0	99	5	4566
mitochondrial matrix	0.0001	5	5.0	99	23	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.

>4x