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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod8

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod8 Module size 40 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 79135 APOO apolipoprotein O 139322 APOOL apolipoprotein O like 388753 COA6 cytochrome c oxidase assembly factor 6 1327 COX4I1 cytochrome c oxidase subunit 4I1 84701 COX4I2 cytochrome c oxidase subunit 4I2 9377 COX5A cytochrome c oxidase subunit 5A 94194 COX5B cytochrome c oxidase subunit 5B 1337 COX6A1 cytochrome c oxidase subunit 6A1 NA COX6A1P2 1339 COX6A2 cytochrome c oxidase subunit 6A2 1340 COX6B1 cytochrome c oxidase subunit 6B1 125965 COX6B2 cytochrome c oxidase subunit 6B2 54322 COX6C cytochrome c oxidase subunit 6C 1346 COX7A1 cytochrome c oxidase subunit 7A1 1347 COX7A2 cytochrome c oxidase subunit 7A2 9167 COX7A2L cytochrome c oxidase subunit 7A2 like 1349 COX7B cytochrome c oxidase subunit 7B 100188937 COX7C cytochrome c oxidase subunit 7C 1351 COX8A cytochrome c oxidase subunit 8A 1537 CYC1 cytochrome c1 54205 CYCS cytochrome c, somatic 10553 HTATIP2 HIV-1 Tat interactive protein 2 4512 MT-CO1 cytochrome c oxidase subunit I 4513 MT-CO2 cytochrome c oxidase subunit II 4514 MT-CO3 cytochrome c oxidase III 4519 MT-CYB cytochrome b 4706 NDUFAB1 NADH:ubiquinone oxidoreductase subunit AB1 681418 NDUFB10 NADH:ubiquinone oxidoreductase subunit B10 100532726 NDUFC2-KCTD14 NDUFC2-KCTD14 readthrough 57407 NMRAL1 NmrA like redox sensor 1 100131801 PET100 PET100 homolog 6392 SDHD succinate dehydrogenase complex subunit D 29796 UQCR10 ubiquinol-cytochrome c reductase, complex III subunit X 10975 UQCR11 ubiquinol-cytochrome c reductase, complex III subunit XI 7381 UQCRB ubiquinol-cytochrome c reductase binding protein 7384 UQCRC1 ubiquinol-cytochrome c reductase core protein 1 7385 UQCRC2 ubiquinol-cytochrome c reductase core protein 2 7386 UQCRFS1 ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 7388 UQCRH ubiquinol-cytochrome c reductase hinge protein 27089 UQCRQ ubiquinol-cytochrome c reductase complex III subunit VII

Functional annotation

Modules were tested for enrichment in functional and pathway annotations using two complementary approaches:
1. To select a small number of specific / non-redundant annotations for each module, a regression-based approach was used;
2. To obtain the complete set of enriched annotations, an extension of Fisher’s exact test that takes annotation bias into account was employed (Wallenius’ non-central hypergeometric distribution).

Most specific annotations for this module

Coeff.1 P-value.2 Source.3 Term.4 Class.5 2.88e-01 1.47e-20 GO ubiquinol-cytochrome-c reductase activity molecular_function 2.42e-01 6.34e-28 GO mitochondrial electron transport, cytochrome c to oxygen biological_process 2.06e-01 1.78e-37 GO cytochrome-c oxidase activity molecular_function 1.34e-01 3.08e-24 GO mitochondrial respiratory chain complex III cellular_component 1.28e-01 5.16e-30 GO mitochondrial respiratory chain complex IV cellular_component 1.22e-01 4.41e-55 Reactome Respiratory electron transport Metabolism 7.34e-02 1.18e-21 GO mitochondrial electron transport, ubiquinol to cytochrome c biological_process 5.59e-02 5.97e-16 GO mitochondrial respiratory chain cellular_component 4.43e-02 1.79e-04 GO MICOS complex cellular_component 1.48e-02 1.39e-15 GO generation of precursor metabolites and energy biological_process 1.13e-02 7.74e-24 Reactome TP53 Regulates Metabolic Genes Gene expression (Transcription) 7.91e-03 6.90e-52 Reactome Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. Metabolism 5.15e-03 1.76e-06 GO regulation of oxidative phosphorylation biological_process

¹Regression coefficient

²Fisher’s exact test nominal P-value

³Annotation source (Reactome, GO biological process (BP), molecular function (MF) and cellular component (CC))

⁴GO category or Reactome pathway

⁵High-level branch of annotation tree

Gene membership

All enriched annotations

Gene Ontology

P-value1 FDR2 Term 0e+00 0e+00 generation of precursor metabolites and energy 0e+00 0e+00 proton transport 0e+00 0e+00 monovalent inorganic cation transport 0e+00 0e+00 purine nucleotide metabolic process 0e+00 0e+00 energy derivation by oxidation of organic compounds 0e+00 0e+00 nucleobase-containing small molecule metabolic process 0e+00 0e+00 respiratory electron transport chain 0e+00 0e+00 ribonucleotide metabolic process 0e+00 0e+00 hydrogen ion transmembrane transport 0e+00 0e+00 mitochondrial electron transport, cytochrome c to oxygen 0e+00 0e+00 cellular respiration 0e+00 0e+00 ATP synthesis coupled electron transport 0e+00 0e+00 electron transport chain 0e+00 0e+00 mitochondrial ATP synthesis coupled electron transport 0e+00 0e+00 nucleotide metabolic process 0e+00 0e+00 oxidative phosphorylation 0e+00 0e+00 cation transmembrane transport 0e+00 0e+00 ATP metabolic process 0e+00 0e+00 aerobic respiration 0e+00 0e+00 mitochondrial electron transport, ubiquinol to cytochrome c

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0e+00 RESPIRATORY ELECTRON TRANSPORT ATP SYNTHESIS BY CHEMIOSMOTIC COUPLING AND HEAT PRODUCTION BY UNCOUPLING PROTEINS 0.00e+00 0e+00 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 0.00e+00 0e+00 RESPIRATORY ELECTRON TRANSPORT 0.00e+00 0e+00 RESPIRATORY ELECTRON TRANSPORT ATP SYNTHESIS BY CHEMIOSMOTIC COUPLING AND HEAT PRODUCTION BY UNCOUPLING PROTEINS 0.00e+00 0e+00 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 0.00e+00 0e+00 RESPIRATORY ELECTRON TRANSPORT 3.73e-02 1e+00 MITOCHONDRIAL PROTEIN IMPORT

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.52e-04 4.01e-01 abnormal cellular respiration 3.35e-04 4.79e-01 abnormal respiratory electron transport chain 1.87e-03 1.00e+00 midbrain hyperplasia 1.87e-03 1.00e+00 increased uterus leiomyoma incidence 1.90e-03 1.00e+00 decreased diastolic filling velocity 3.74e-03 1.00e+00 abnormal carotid body morphology 3.75e-03 1.00e+00 abnormal viscerocranium morphology 5.61e-03 1.00e+00 cranioschisis 5.61e-03 1.00e+00 abnormal dorsoventral coat patterning 7.47e-03 1.00e+00 absent pre-B cells 7.48e-03 1.00e+00 bidirectional circling 7.48e-03 1.00e+00 increased ovary tumor incidence 7.48e-03 1.00e+00 increased malignant tumor incidence 7.48e-03 1.00e+00 abnormal survival 9.34e-03 1.00e+00 abnormal mouth morphology 9.35e-03 1.00e+00 forebrain hypoplasia 9.35e-03 1.00e+00 intracerebral hemorrhage 1.12e-02 1.00e+00 abnormal mammary gland morphology 1.12e-02 1.00e+00 increased hemangiosarcoma incidence 1.12e-02 1.00e+00 increased metastatic potential

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)