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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod27

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod27 Module size 29 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 131474 CHCHD4 coiled-coil-helix-coiled-coil-helix domain containing 4 100529144 CORO7-PAM16 CORO7-PAM16 readthrough 131118 DNAJC19 DnaJ heat shock protein family (Hsp40) member C19 10989 IMMT inner membrane mitochondrial protein 4580 MTX1 metaxin 1 10651 MTX2 metaxin 2 345778 MTX3 metaxin 3 51025 PAM16 presequence translocase associated motor 16 25813 SAMM50 SAMM50 sorting and assembly machinery component 81855 SFXN3 sideroflexin 3 83447 SLC25A31 solute carrier family 25 member 31 293 SLC25A6 solute carrier family 25 member 6 10440 TIMM17A translocase of inner mitochondrial membrane 17A 10245 TIMM17B translocase of inner mitochondrial membrane 17B 29090 TIMM21 translocase of inner mitochondrial membrane 21 29928 TIMM22 translocase of inner mitochondrial membrane 22 100287932 TIMM23 translocase of inner mitochondrial membrane 23 100652748 TIMM23B translocase of inner mitochondrial membrane 23 homolog B 10469 TIMM44 translocase of inner mitochondrial membrane 44 92609 TIMM50 translocase of inner mitochondrial membrane 50 9804 TOMM20 translocase of outer mitochondrial membrane 20 387990 TOMM20L translocase of outer mitochondrial membrane 20 like 56993 TOMM22 translocase of outer mitochondrial membrane 22 10452 TOMM40 translocase of outer mitochondrial membrane 40 84134 TOMM40L translocase of outer mitochondrial membrane 40 like 401505 TOMM5 translocase of outer mitochondrial membrane 5 29964 TOMM6 prickle planar cell polarity protein 4 54543 TOMM7 translocase of outer mitochondrial membrane 7 9868 TOMM70A translocase of outer mitochondrial membrane 70

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 2.77e-01 1.37e-21 GO mitochondrial outer membrane translocase complex cellular_component 2.60e-01 4.91e-35 GO protein import into mitochondrial matrix biological_process 2.52e-01 3.74e-22 GO mitochondrial inner membrane presequence translocase complex cellular_component 1.41e-01 9.93e-29 GO protein transmembrane transporter activity molecular_function 9.25e-02 3.17e-45 Reactome Mitochondrial protein import Metabolism of proteins 3.87e-02 9.80e-28 GO protein targeting to mitochondrion biological_process 1.02e-02 1.26e-07 Reactome Cristae formation Organelle biogenesis and maintenance

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 protein transmembrane transport 0e+00 0e+00 protein import into mitochondrial matrix 0e+00 0e+00 intracellular protein transmembrane transport 0e+00 0e+00 mitochondrion organization 0e+00 0e+00 mitochondrial membrane organization 0e+00 0e+00 protein targeting to mitochondrion 0e+00 0e+00 establishment of protein localization to organelle 0e+00 0e+00 protein targeting 0e+00 0e+00 mitochondrial transmembrane transport 0e+00 0e+00 mitochondrial transport 0e+00 0e+00 protein localization to mitochondrion 0e+00 0e+00 establishment of protein localization to mitochondrion 0e+00 0e+00 protein localization to organelle 0e+00 0e+00 protein import 0e+00 0e+00 mitochondrial membrane 0e+00 0e+00 integral component of mitochondrial membrane 0e+00 0e+00 mitochondrial outer membrane 0e+00 0e+00 mitochondrial envelope 0e+00 0e+00 outer membrane 0e+00 0e+00 mitochondrial outer membrane translocase complex

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 MITOCHONDRIAL PROTEIN IMPORT 0.00e+00 0.00e+00 MITOCHONDRIAL PROTEIN IMPORT 5.45e-03 4.40e-01 INTERACTIONS OF VPR WITH HOST CELLULAR PROTEINS 6.88e-03 5.92e-01 INTERACTIONS OF VPR WITH HOST CELLULAR PROTEINS 1.11e-02 7.97e-01 HOST INTERACTIONS OF HIV FACTORS 1.73e-02 1.00e+00 HOST INTERACTIONS OF HIV FACTORS 2.90e-02 1.00e+00 REGULATION OF INSULIN SECRETION 2.99e-02 1.00e+00 REGULATION OF INSULIN SECRETION 3.15e-02 1.00e+00 HIV INFECTION 4.04e-02 1.00e+00 INTEGRATION OF ENERGY METABOLISM 4.81e-02 1.00e+00 HIV INFECTION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.88e-03 1e+00 premature aging 3.82e-03 1e+00 kyphosis 5.70e-03 1e+00 alopecia 7.50e-03 1e+00 abnormal spermatocyte morphology 2.24e-02 1e+00 arrest of male meiosis 2.79e-02 1e+00 decreased lumbar vertebrae number 2.82e-02 1e+00 decreased grip strength 2.97e-02 1e+00 increased sacral vertebrae number 2.99e-02 1e+00 abnormal male germ cell apoptosis 3.40e-02 1e+00 small testis 4.31e-02 1e+00 decreased testis weight

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

²FDR corrected p-value (Benjamini-Hochberg)