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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod327

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod327 Module size 31 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 498 ATP5A1 ATP synthase F1 subunit alpha 506 ATP5B ATP synthase F1 subunit beta 509 ATP5C1 ATP synthase F1 subunit gamma 513 ATP5D ATP synthase F1 subunit delta 514 ATP5E ATP synthase F1 subunit epsilon 432369 ATP5EP2 ATP synthase F1 subunit epsilon pseudogene 2 515 ATP5F1 ATP synthase peripheral stalk-membrane subunit b 516 ATP5G1 ATP synthase membrane subunit c locus 1 517 ATP5G2 ATP synthase membrane subunit c locus 2 518 ATP5G3 ATP synthase membrane subunit c locus 3 10476 ATP5H ATP synthase peripheral stalk subunit d 521 ATP5I ATP synthase membrane subunit e 522 ATP5J ATP synthase peripheral stalk subunit F6 9551 ATP5J2 ATP synthase membrane subunit f 100526740 ATP5J2-PTCD1 ATP5MF-PTCD1 readthrough 10632 ATP5L ATP synthase membrane subunit g 267020 ATP5L2 ATP synthase membrane subunit g like 539 ATP5O ATP synthase peripheral stalk subunit OSCP 27109 ATP5S distal membrane arm assembly complex 2 like 93974 ATPIF1 ATP synthase inhibitory factor subunit 1 9556 C14orf2 ATP synthase membrane subunit 6.8PL 55847 CISD1 CDGSH iron sulfur domain 1 493856 CISD2 CDGSH iron sulfur domain 2 257019 FRMD3 FERM domain containing 3 4508 MT-ATP6 ATP synthase F0 subunit 6 4509 MT-ATP8 ATP synthase F0 subunit 8 80298 MTERFD3 mitochondrial transcription termination factor 2 150678 MYEOV2 COP9 signalosome subunit 9 4696 NDUFA3 NADH:ubiquinone oxidoreductase subunit A3 26024 PTCD1 pentatricopeptide repeat domain 1 84833 USMG5 ATP synthase membrane subunit DAPIT

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 2.25e-01 1.59e-19 GO mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) cellular_component 1.63e-01 1.29e-28 GO mitochondrial proton-transporting ATP synthase complex cellular_component 1.18e-01 1.99e-23 GO mitochondrial ATP synthesis coupled proton transport biological_process 8.71e-02 1.29e-12 GO proton transmembrane transporter activity molecular_function 4.44e-02 2.50e-26 Reactome Formation of ATP by chemiosmotic coupling 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 0e+00 0e+00 proton transport 0e+00 0e+00 ribonucleoside monophosphate biosynthetic process 0e+00 0e+00 monovalent inorganic cation transport 0e+00 0e+00 purine nucleotide metabolic process 0e+00 0e+00 purine nucleotide biosynthetic process 0e+00 0e+00 ribonucleotide metabolic process 0e+00 0e+00 ATP hydrolysis coupled cation transmembrane transport 0e+00 0e+00 mitochondrial ATP synthesis coupled proton transport 0e+00 0e+00 nucleotide metabolic process 0e+00 0e+00 mitochondrial transmembrane transport 0e+00 0e+00 mitochondrial transport 0e+00 0e+00 cation transmembrane transport 0e+00 0e+00 purine-containing compound biosynthetic process 0e+00 0e+00 ATP synthesis coupled proton transport 0e+00 0e+00 nucleobase-containing small molecule metabolic process 0e+00 0e+00 nucleotide biosynthetic process 0e+00 0e+00 nucleoside triphosphate biosynthetic process 0e+00 0e+00 ATP hydrolysis coupled transmembrane transport 0e+00 0e+00 hydrogen ion transmembrane transport 0e+00 0e+00 nucleoside monophosphate biosynthetic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 FORMATION OF ATP BY CHEMIOSMOTIC COUPLING 0.00e+00 0.00e+00 RESPIRATORY ELECTRON TRANSPORT ATP SYNTHESIS BY CHEMIOSMOTIC COUPLING AND HEAT PRODUCTION BY UNCOUPLING PROTEINS 0.00e+00 0.00e+00 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 0.00e+00 0.00e+00 FORMATION OF ATP BY CHEMIOSMOTIC COUPLING 0.00e+00 0.00e+00 RESPIRATORY ELECTRON TRANSPORT ATP SYNTHESIS BY CHEMIOSMOTIC COUPLING AND HEAT PRODUCTION BY UNCOUPLING PROTEINS 0.00e+00 0.00e+00 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 1.81e-05 2.61e-03 MITOCHONDRIAL PROTEIN IMPORT 6.94e-05 1.12e-02 MITOCHONDRIAL PROTEIN IMPORT

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.65e-03 1e+00 decreased lean body mass 3.11e-03 1e+00 abnormal behavior 5.64e-03 1e+00 dilated sarcoplasmic reticulum 5.64e-03 1e+00 decreased tidal volume 7.50e-03 1e+00 retinal neovascularization 7.50e-03 1e+00 abnormal mitochondrial shape 7.50e-03 1e+00 decreased fluid intake 7.51e-03 1e+00 abnormal respiratory function 9.38e-03 1e+00 increased mitochondria size 9.39e-03 1e+00 abnormal skeletal muscle fiber type ratio 1.12e-02 1e+00 small thoracic cavity 1.12e-02 1e+00 decreased body mass index 1.12e-02 1e+00 abnormal eye size 1.13e-02 1e+00 abnormal sarcomere morphology 1.31e-02 1e+00 decreased carbon dioxide production 1.31e-02 1e+00 abnormal defecation 1.31e-02 1e+00 oliguria 1.31e-02 1e+00 abnormal mitochondrial crista morphology 1.44e-02 1e+00 abnormal mitochondrial ATP synthesis coupled electron transport 1.47e-02 1e+00 abnormal respiratory quotient

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

²FDR corrected p-value (Benjamini-Hochberg)