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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod187

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod187 Module size 61 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 7920 ABHD16A abhydrolase domain containing 16A 64756 ATPAF1 ATP synthase mitochondrial F1 complex assembly factor 1 91647 ATPAF2 ATP synthase mitochondrial F1 complex assembly factor 2 154791 C7orf55 formation of mitochondrial complex V assembly factor 1 homolog 400916 CHCHD10 coiled-coil-helix-coiled-coil-helix domain containing 10 51142 CHCHD2 coiled-coil-helix-coiled-coil-helix domain containing 2 54927 CHCHD3 coiled-coil-helix-coiled-coil-helix domain containing 3 84303 CHCHD6 coiled-coil-helix-coiled-coil-helix domain containing 6 79145 CHCHD7 coiled-coil-helix-coiled-coil-helix domain containing 7 55744 COA1 cytochrome c oxidase assembly factor 1 homolog 28958 COA3 cytochrome c oxidase assembly factor 3 1352 COX10 cytochrome c oxidase assembly factor heme A:farnesyltransferase COX10 1353 COX11 cytochrome c oxidase copper chaperone COX11 84987 COX14 cytochrome c oxidase assembly factor COX14 1355 COX15 cytochrome c oxidase assembly homolog COX15 100302447 COX16 cytochrome c oxidase assembly factor COX16 89786 COX17 cytochrome c oxidase copper chaperone COX17 170712 COX7B2 cytochrome c oxidase subunit 7B2 341947 COX8C cytochrome c oxidase subunit 8C 84418 CYSTM1 cysteine rich transmembrane module containing 1 2108 ETFA electron transfer flavoprotein subunit alpha 2109 ETFB electron transfer flavoprotein subunit beta 2110 ETFDH electron transfer flavoprotein dehydrogenase 10712 FAM189B family with sequence similarity 189 member B 9052 GPRC5A G protein-coupled receptor class C group 5 member A 3052 HCCS holocytochrome c synthase 192286 HIGD2A HIG1 hypoxia inducible domain family member 2A 3141 HLCS holocarboxylase synthetase 8649 LAMTOR3 late endosomal/lysosomal adaptor, MAPK and MTOR activator 3 90624 LYRM7 LYR motif containing 7 440574 MINOS1 mitochondrial inner membrane organizing system 1 84300 MNF1 ubiquinol-cytochrome c reductase complex assembly factor 2 4358 MPV17 mitochondrial inner membrane protein MPV17 10232 MSLN mesothelin 25915 NDUFAF3 NADH:ubiquinone oxidoreductase complex assembly factor 3 29078 NDUFAF4 NADH:ubiquinone oxidoreductase complex assembly factor 4 55471 NDUFAF7 NADH:ubiquinone oxidoreductase complex assembly factor 7 55335 NIPSNAP3B nipsnap homolog 3B 5018 OXA1L OXA1L, mitochondrial inner membrane protein 51449 PCYOX1 prenylcysteine oxidase 1 23203 PMPCA peptidase, mitochondrial processing alpha subunit 9512 PMPCB peptidase, mitochondrial processing beta subunit 51195 RAPGEFL1 Rap guanine nucleotide exchange factor like 1 6341 SCO1 SCO1, cytochrome c oxidase assembly protein 644096 SDHAF1 succinate dehydrogenase complex assembly factor 1 6390 SDHB succinate dehydrogenase complex iron sulfur subunit B 6391 SDHC succinate dehydrogenase complex subunit C 94081 SFXN1 sideroflexin 1 10165 SLC25A13 solute carrier family 25 member 13 5250 SLC25A3 solute carrier family 25 member 3 90203 SNX21 sorting nexin family member 21 64463 SURF1 SURF1, cytochrome c oxidase assembly factor 7047 TGM4 transglutaminase 4 343641 TGM6 transglutaminase 6 116179 TGM7 transglutaminase 7 51522 TMEM14C transmembrane protein 14C 729515 TMEM242 transmembrane protein 242 55245 UQCC ubiquinol-cytochrome c reductase complex assembly factor 1 7416 VDAC1 voltage dependent anion channel 1 7417 VDAC2 voltage dependent anion channel 2 7419 VDAC3 voltage dependent anion channel 3

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 3.10e-01 1.05e-11 GO respiratory chain complex IV assembly biological_process 2.30e-01 4.90e-07 GO voltage-gated anion channel activity molecular_function 1.71e-01 4.11e-14 GO mitochondrial respiratory chain complex IV assembly biological_process 1.47e-01 2.05e-06 GO protein-glutamine gamma-glutamyltransferase activity molecular_function 1.39e-01 2.05e-06 GO MICOS complex cellular_component 1.09e-01 2.05e-06 GO ubiquinone binding molecular_function 1.02e-01 2.92e-06 GO fatty acid beta-oxidation using acyl-CoA dehydrogenase biological_process 7.58e-02 6.75e-08 GO mitochondrial respiratory chain cellular_component 6.23e-02 6.10e-09 Reactome Mitochondrial calcium ion transport Transport of small molecules 4.23e-02 2.40e-13 Reactome Mitochondrial protein import Metabolism of proteins 3.50e-02 3.30e-12 GO integral component of mitochondrial inner membrane cellular_component 3.32e-02 1.29e-04 GO mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone) cellular_component 1.32e-02 4.02e-10 GO mitochondrial membrane cellular_component 1.29e-02 4.85e-07 GO cellular respiration biological_process 9.30e-03 1.66e-10 Reactome Respiratory electron transport Metabolism

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 0.00e+00 0.00e+00 generation of precursor metabolites and energy 0.00e+00 0.00e+00 cellular respiration 0.00e+00 0.00e+00 mitochondrion organization 0.00e+00 0.00e+00 mitochondrial respiratory chain complex assembly 0.00e+00 0.00e+00 cellular protein complex assembly 0.00e+00 0.00e+00 cytochrome complex assembly 0.00e+00 0.00e+00 respiratory chain complex IV assembly 0.00e+00 0.00e+00 mitochondrial membrane 0.00e+00 0.00e+00 mitochondrial envelope 0.00e+00 0.00e+00 mitochondrial inner membrane 0.00e+00 0.00e+00 organelle inner membrane 0.00e+00 0.00e+00 electron carrier activity 2.48e-11 2.18e-08 energy derivation by oxidation of organic compounds 3.11e-11 2.71e-08 mitochondrial respiratory chain complex IV assembly 4.08e-11 3.52e-08 mitochondrial respiratory chain complex IV biogenesis 5.35e-09 2.53e-06 cytochrome-c oxidase activity 7.84e-09 5.16e-06 respiratory electron transport chain 8.30e-09 5.44e-06 electron transport chain 1.22e-08 4.77e-06 respiratory chain 4.34e-08 2.59e-05 aerobic respiration

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.43e-09 4.64e-07 RESPIRATORY ELECTRON TRANSPORT 8.42e-09 2.49e-06 RESPIRATORY ELECTRON TRANSPORT ATP SYNTHESIS BY CHEMIOSMOTIC COUPLING AND HEAT PRODUCTION BY UNCOUPLING PROTEINS 2.20e-07 5.46e-05 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 2.24e-07 4.20e-05 RESPIRATORY ELECTRON TRANSPORT 5.33e-07 9.73e-05 RESPIRATORY ELECTRON TRANSPORT ATP SYNTHESIS BY CHEMIOSMOTIC COUPLING AND HEAT PRODUCTION BY UNCOUPLING PROTEINS 2.14e-06 3.55e-04 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 2.25e-06 4.77e-04 MITOCHONDRIAL PROTEIN IMPORT 2.83e-06 4.58e-04 MITOCHONDRIAL PROTEIN IMPORT 4.28e-04 5.62e-02 CITRIC ACID CYCLE TCA CYCLE 8.88e-04 9.05e-02 CITRIC ACID CYCLE TCA CYCLE 2.38e-03 2.17e-01 PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE 2.55e-03 2.62e-01 PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE 4.91e-02 1.00e+00 GLUCONEOGENESIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.06e-03 9.29e-01 abnormal respiratory electron transport chain 2.05e-03 1.00e+00 abnormal cued conditioning behavior 3.76e-03 1.00e+00 decreased circulating serum albumin level 3.77e-03 1.00e+00 abnormal portal triad morphology 5.64e-03 1.00e+00 spiral ligament degeneration 5.65e-03 1.00e+00 abnormal renal/urinary system physiology 5.65e-03 1.00e+00 small sebaceous gland 7.49e-03 1.00e+00 decreased thoracic vertebrae number 7.52e-03 1.00e+00 abnormal liver lobule morphology 9.37e-03 1.00e+00 dilated mitochondria 9.39e-03 1.00e+00 cochlear ganglion hypoplasia 1.12e-02 1.00e+00 fused podocyte foot processes 1.13e-02 1.00e+00 abnormal liver sinusoid morphology 1.31e-02 1.00e+00 abnormal scala media morphology 1.52e-02 1.00e+00 embryonic lethality 1.68e-02 1.00e+00 stria vascularis degeneration 1.68e-02 1.00e+00 decreased mitochondrial DNA content 1.68e-02 1.00e+00 extended life span 1.69e-02 1.00e+00 cortical renal glomerulopathies 1.69e-02 1.00e+00 decreased cellular hemoglobin content

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

²FDR corrected p-value (Benjamini-Hochberg)