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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod127

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod127 Module size 43 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 4535 MT-ND1 NADH dehydrogenase, subunit 1 (complex I) 4536 MT-ND2 MTND2 4537 MT-ND3 NADH dehydrogenase, subunit 3 (complex I) 4538 MT-ND4 NADH dehydrogenase, subunit 4 (complex I) 4539 MT-ND4L NADH dehydrogenase, subunit 4L (complex I) 4540 MT-ND5 NADH dehydrogenase, subunit 5 (complex I) 4541 MT-ND6 NADH dehydrogenase, subunit 6 (complex I) 4694 NDUFA1 NADH:ubiquinone oxidoreductase subunit A1 4705 NDUFA10 NADH:ubiquinone oxidoreductase subunit A10 126328 NDUFA11 NADH:ubiquinone oxidoreductase subunit A11 100910710 NDUFA12 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12-like 51079 NDUFA13 NADH:ubiquinone oxidoreductase subunit A13 4695 NDUFA2 NADH:ubiquinone oxidoreductase subunit A2 4697 NDUFA4 NDUFA4, mitochondrial complex associated 4698 NDUFA5 NADH:ubiquinone oxidoreductase subunit A5 4700 NDUFA6 NADH:ubiquinone oxidoreductase subunit A6 4701 NDUFA7 NADH:ubiquinone oxidoreductase subunit A7 4702 NDUFA8 NADH:ubiquinone oxidoreductase subunit A8 4704 NDUFA9 NADH:ubiquinone oxidoreductase subunit A9 51103 NDUFAF1 NADH:ubiquinone oxidoreductase complex assembly factor 1 4707 NDUFB1 NADH:ubiquinone oxidoreductase subunit B1 54539 NDUFB11 NADH:ubiquinone oxidoreductase subunit B11 4708 NDUFB2 NADH:ubiquinone oxidoreductase subunit B2 4709 NDUFB3 NADH:ubiquinone oxidoreductase subunit B3 4710 NDUFB4 NADH:ubiquinone oxidoreductase subunit B4 4711 NDUFB5 NADH:ubiquinone oxidoreductase subunit B5 4712 NDUFB6 NADH:ubiquinone oxidoreductase subunit B6 4713 NDUFB7 NADH:ubiquinone oxidoreductase subunit B7 4714 NDUFB8 NADH:ubiquinone oxidoreductase subunit B8 4715 NDUFB9 NADH:ubiquinone oxidoreductase subunit B9 4717 NDUFC1 NADH:ubiquinone oxidoreductase subunit C1 4718 NDUFC2 NADH:ubiquinone oxidoreductase subunit C2 4719 NDUFS1 NADH:ubiquinone oxidoreductase core subunit S1 4720 NDUFS2 NADH:ubiquinone oxidoreductase core subunit S2 4722 NDUFS3 NADH:ubiquinone oxidoreductase core subunit S3 4724 NDUFS4 NADH:ubiquinone oxidoreductase subunit S4 4725 NDUFS5 NADH:ubiquinone oxidoreductase subunit S5 4726 NDUFS6 NADH:ubiquinone oxidoreductase subunit S6 374291 NDUFS7 NADH:ubiquinone oxidoreductase core subunit S7 4728 NDUFS8 NADH:ubiquinone oxidoreductase core subunit S8 4723 NDUFV1 NADH:ubiquinone oxidoreductase core subunit V1 4729 NDUFV2 NADH:ubiquinone oxidoreductase core subunit V2 4731 NDUFV3 NADH:ubiquinone oxidoreductase subunit V3

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 2.43e-01 1.37e-115 GO mitochondrial respiratory chain complex I cellular_component 2.38e-01 3.95e-111 GO NADH dehydrogenase (ubiquinone) activity molecular_function 1.74e-01 4.37e-104 GO mitochondrial electron transport, NADH to ubiquinone biological_process 1.63e-01 3.22e-109 Reactome Complex I biogenesis Metabolism 1.31e-02 1.57e-23 GO NADH dehydrogenase activity molecular_function 1.41e-03 1.08e-100 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 0e+00 0e+00 purine nucleotide metabolic process 0e+00 0e+00 mitochondrial electron transport, NADH to ubiquinone 0e+00 0e+00 respiratory electron transport chain 0e+00 0e+00 ribonucleotide metabolic process 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 cellular protein complex assembly 0e+00 0e+00 nucleotide metabolic process 0e+00 0e+00 mitochondrial respiratory chain complex I biogenesis 0e+00 0e+00 oxidative phosphorylation 0e+00 0e+00 mitochondrial respiratory chain complex I assembly 0e+00 0e+00 generation of precursor metabolites and energy 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 cellular respiration 0e+00 0e+00 mitochondrion organization 0e+00 0e+00 ATP metabolic process 0e+00 0e+00 mitochondrial respiratory chain complex assembly 0e+00 0e+00 mitochondrial respiratory chain complex I

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 RESPIRATORY ELECTRON TRANSPORT ATP SYNTHESIS BY CHEMIOSMOTIC COUPLING AND HEAT PRODUCTION BY UNCOUPLING PROTEINS 0e+00 0e+00 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 0e+00 0e+00 RESPIRATORY ELECTRON TRANSPORT 0e+00 0e+00 RESPIRATORY ELECTRON TRANSPORT ATP SYNTHESIS BY CHEMIOSMOTIC COUPLING AND HEAT PRODUCTION BY UNCOUPLING PROTEINS 0e+00 0e+00 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 0e+00 0e+00 RESPIRATORY ELECTRON TRANSPORT

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.66e-04 3.13e-01 abnormal mitochondrial crista morphology 2.75e-04 4.28e-01 abnormal respiratory electron transport chain 1.88e-03 1.00e+00 positive geotaxis 3.48e-03 1.00e+00 increased heart weight 3.75e-03 1.00e+00 increased heart right ventricle weight 3.75e-03 1.00e+00 abnormal cerebellum lobule morphology 3.75e-03 1.00e+00 increased circulating carnitine level 3.76e-03 1.00e+00 brainstem hemorrhage 5.61e-03 1.00e+00 decreased circulating creatine kinase level 5.62e-03 1.00e+00 hyperekplexia 5.64e-03 1.00e+00 optic nerve atrophy 5.64e-03 1.00e+00 abnormal olfactory bulb external plexiform layer morphology 5.64e-03 1.00e+00 abnormal pulmonary ventilation 5.64e-03 1.00e+00 straub tail 7.50e-03 1.00e+00 abnormal mitochondrial shape 9.36e-03 1.00e+00 decreased left ventricle systolic pressure 9.37e-03 1.00e+00 increased left ventricle diastolic pressure 9.37e-03 1.00e+00 tail dragging 9.37e-03 1.00e+00 abnormal muscle tone 9.38e-03 1.00e+00 axonal spheroids

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

²FDR corrected p-value (Benjamini-Hochberg)