Module 152 -- Oxidative phosphorylation and ATP synthesis

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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: 23
Num genes: 124 (see 1706 additional genes for this module)
Num experiments: 291 (135 induced, 156 repressed)
Parent module: None
Children modules: 62 103 77 116


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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.
nucleoside monophosphate phosphorylation
ATP_Synthesis
proton transport
mitochondrial inner membrane
cytochrome c oxidase activity
cbb3_type cytochrome c oxidase
NADH dehydrogenase activity
NADH dehydrogenase (ubiquinone) activity
Ubiquinone_biosynthesis
protein_disulfide reduction
mitochondrial electron transport, NADH to ubiquinone
ATP synthesis coupled electron transport (sensu Eukarya)
oxidative phosphorylation
mitochondrion
ion transporter activity
mitochondrial membrane
inner membrane
hydrogen ion transporter activity
Oxidative_phosphorylation
monovalent inorganic cation transporter activity
sodium ion transporter activity
metal ion transporter activity
Electron Transport Chain


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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
Prostate (Prostate cancer*) Prostate cancer* 3.5e-21 41 26.4 155 101 1945
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 4.8e-11 20 14.8 135 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 4.8e-11 20 14.8 135 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 4.8e-11 20 14.8 135 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 4.8e-11 20 14.8 135 53 1945
Lung carcinoid (Lung cancer) Lung cancer 2.9e-08 9 60 15 20 276
CNS cancer or cell line (Neuro tumors*) Neuro tumors* 1.0e-07 22 14.1 155 81 1945
CNS tumor (Neuro tumors*) Neuro tumors* 1.0e-07 22 14.1 155 81 1945
CNS tissue, cancer or cell line (Neuro tumors*) Neuro tumors* 2.5e-07 22 14.1 155 85 1945
Cancer and cell line (Neuro tumors*) Neuro tumors* 3.2e-07 22 14.1 155 86 1945
Cancer (Neuro tumors*) Neuro tumors* 3.2e-07 22 14.1 155 86 1945
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 7.4e-06 15 9.6 155 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 7.4e-06 15 9.6 155 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 7.4e-06 15 9.6 155 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 7.4e-06 15 9.6 155 53 1945
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 1.2e-05 6 100 6 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 1.2e-05 6 100 6 30 182
Metastasis (Liver cancer) Liver cancer 6.2e-05 6 30 20 10 207
Follicular lymphoma (B lymphoma) B lymphoma 0.0001 8 47.0 17 28 245
Follicular lymphoma (Various tumors) Various tumors 0.0001 5 38.4 13 9 154


Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
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
mitochondrion 1.3e-134 103 88.0 117 207 4566
monovalent inorganic cation transporter activity 4.4e-88 61 52.1 117 80 4566
ion transporter activity 3.1e-72 65 55.5 117 144 4566
sodium ion transporter activity 1.1e-57 40 34.1 117 50 4566
metal ion transporter activity 2.6e-56 42 35.8 117 60 4566
hydrogen ion transporter activity 4.4e-53 38 32.4 117 50 4566
mitochondrial membrane 8.2e-41 33 28.2 117 54 4566
electron transporter activity 4.2e-38 55 47.0 117 269 4566
inner membrane 2.4e-37 25 21.3 117 29 4566
oxidoreductase activity 8.7e-36 52 44.4 117 254 4566
NADH dehydrogenase (ubiquinone) activity 6.3e-35 23 19.6 117 26 4566
NADH dehydrogenase activity 2.7e-33 22 18.8 117 25 4566
proton transport 1.4e-27 22 18.8 117 35 4566
mitochondrial inner membrane 3.6e-27 23 19.6 117 41 4566
electron transport 3.0e-24 32 27.3 117 128 4566
energy pathways 4.0e-23 37 31.6 117 200 4566
cation transporter activity 1.3e-22 21 17.9 117 45 4566
photosynthesis 6.1e-22 33 28.2 117 162 4566
oxidative phosphorylation 1.5e-20 14 11.9 117 17 4566
nucleoside monophosphate phosphorylation 6.7e-20 14 11.9 117 18 4566
monovalent inorganic cation transport 4.1e-19 23 19.6 117 79 4566
cytochrome c oxidase activity 5.7e-19 12 10.2 117 13 4566
phosphorus metabolism 1.5e-18 28 23.9 117 138 4566
ATP synthesis coupled electron transport (sensu Eukarya) 1.9e-17 12 10.2 117 15 4566
cbb3-type cytochrome c oxidase 2.2e-17 11 9.4 117 12 4566
phosphate metabolism 2.7e-17 28 23.9 117 153 4566
cation transport 7.0e-17 25 21.3 117 120 4566
protein-disulfide reduction 7.5e-17 12 10.2 117 16 4566
mitochondrial electron transport\, NADH to ubiquinone 6.6e-16 11 9.4 117 14 4566
phosphorylation 1.2e-15 28 23.9 117 176 4566
proton-transporting ATP synthase complex (sensu Eukarya) 3.4e-14 9 7.6 117 10 4566
photosynthesis\, light reaction 4.2e-14 22 18.8 117 115 4566
ion transport 4.9e-13 26 22.2 117 188 4566
mitochondrial electron transport chain 1.2e-12 8 6.8 117 9 4566
vacuolar hydrogen-transporting ATPase 6.3e-12 8 6.8 117 10 4566
nucleotide metabolism 3.0e-11 15 12.8 117 64 4566
ubiquinol-cytochrome c reductase activity 1.0e-08 5 4.2 117 5 4566
membrane fraction 2.5e-08 26 22.2 117 304 4566
outer membrane 6.3e-07 6 5.1 117 14 4566
ammonia oxidation 2.0e-06 4 3.4 117 5 4566
hydrogen-exporting ATPase activity\, phosphorylative mechanism 5.9e-06 4 3.4 117 6 4566
tricarboxylic acid cycle 2.4e-05 5 4.2 117 15 4566
ATP-binding and phosphorylation-dependent chloride channel activity 6.4e-05 3 2.5 117 4 4566


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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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