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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod140

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod140 Module size 76 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 284615 ANKRD34A ankyrin repeat domain 34A 79096 C11orf49 chromosome 11 open reading frame 49 57102 C12orf4 chromosome 12 open reading frame 4 160419 C12orf50 chromosome 12 open reading frame 50 84984 CEP19 centrosomal protein 19 4359 CHM myelin protein zero 57053 CHRNA10 cholinergic receptor nicotinic alpha 10 subunit 100529261 CHURC1-FNTB CHURC1-FNTB readthrough 10260 DENND4A DENN domain containing 4A 55667 DENND4C DENN domain containing 4C 201627 DENND6A DENN domain containing 6A 8411 EEA1 early endosome antigen 1 23086 EXPH5 exophilin 5 285172 FAM126B family with sequence similarity 126 member B 780776 FAM18A trans-golgi network vesicle protein 23 homolog A 51030 FAM18B1 trans-golgi network vesicle protein 23 homolog B 201158 FAM18B2 trans-golgi network vesicle protein 23 homolog C 100533496 FAM18B2-CDRT4 TVP23C-CDRT4 readthrough 196472 FAM71C family with sequence similarity 71 member C 2339 FNTA farnesyltransferase, CAAX box, alpha 2342 FNTB farnesyltransferase, CAAX box, beta 2801 GOLGA2 golgin A2 2804 GOLGB1 golgin B1 64689 GORASP1 golgi reassembly stacking protein 1 26003 GORASP2 golgi reassembly stacking protein 2 3382 ICA1 islet cell autoantigen 1 130026 ICA1L islet cell autoantigen 1 like 293688 ICMT transmembrane 7 superfamily member 2 51124 IER3IP1 immediate early response 3 interacting protein 1 154881 KCTD7 potassium channel tetramerization domain containing 7 3886 KRT35 keratin 35 25875 LETMD1 LETM1 domain containing 1 57106 NAT14 N-acetyltransferase 14 (putative) 26960 NBEA neurobeachin 65009 NDRG4 NDRG family member 4 115209 OMA1 OMA1 zinc metallopeptidase 27445 PCLO piccolo presynaptic cytomatrix protein 5229 PGGT1B protein geranylgeranyltransferase type I subunit beta 80223 RAB11FIP1 RAB11 family interacting protein 1 22841 RAB11FIP2 RAB11 family interacting protein 2 9727 RAB11FIP3 RAB11 family interacting protein 3 84440 RAB11FIP4 RAB11 family interacting protein 4 26056 RAB11FIP5 RAB11 family interacting protein 5 115273 RAB42 RAB42, member RAS oncogene family 79874 RABEP2 rabaptin, RAB GTPase binding effector protein 2 27342 RABGEF1 RAB guanine nucleotide exchange factor 1 5875 RABGGTA Rab geranylgeranyltransferase subunit alpha 65055 REEP1 receptor accessory protein 1 221035 REEP3 receptor accessory protein 3 80346 REEP4 receptor accessory protein 4 7905 REEP5 receptor accessory protein 5 92840 REEP6 receptor accessory protein 6 440804 RIMBP3B RIMS binding protein 3B 54453 RIN2 Ras and Rab interactor 2 79890 RIN3 Ras and Rab interactor 3 126432 RINL Ras and Rab interactor like 80230 RUFY1 RUN and FYVE domain containing 1 10900 RUNDC3A RUN domain containing 3A 9853 RUSC2 RUN and SH3 domain containing 2 55972 SLC25A40 solute carrier family 25 member 40 728661 SLC35E2B solute carrier family 35 member E2B 55773 TBC1D23 TBC1 domain family member 23 9779 TBC1D5 TBC1 domain family member 5 93627 TBCK TBC1 domain containing kinase 284114 TMEM102 transmembrane protein 102 153339 TMEM167A transmembrane protein 167A 56900 TMEM167B transmembrane protein 167B 388021 TMEM179 transmembrane protein 179 7110 TMF1 TATA element modulatory factor 1 57705 WDFY4 WDFY family member 4 124997 WDR81 WD repeat domain 81 54432 YIPF1 Yip1 domain family member 1 78992 YIPF2 Yip1 domain family member 2 60685 ZFAND3 zinc finger AN1-type containing 3 54469 ZFAND6 zinc finger AN1-type containing 6 57732 ZFYVE28 zinc finger FYVE-type containing 28

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 4.22e-01 2.01e-09 GO protein geranylgeranylation biological_process 6.73e-02 1.44e-05 Reactome Golgi Cisternae Pericentriolar Stack Reorganization Cell Cycle 5.87e-02 3.31e-04 GO ADP-ribosylation factor binding molecular_function 4.39e-02 2.66e-05 GO regulated exocytosis biological_process 3.88e-02 2.24e-08 GO Rab guanyl-nucleotide exchange factor activity molecular_function 3.02e-03 9.13e-04 GO endoplasmic reticulum tubular network cellular_component 1.36e-03 3.53e-07 GO endocytosis 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 0.00e+00 0.00e+00 GTPase binding 0.00e+00 0.00e+00 small GTPase binding 0.00e+00 0.00e+00 Rab GTPase binding 0.00e+00 0.00e+00 Ras GTPase binding 0.00e+00 0.00e+00 protein prenyltransferase activity 3.15e-12 2.89e-09 protein prenylation 9.51e-12 6.34e-09 prenyltransferase activity 1.51e-09 7.77e-07 protein geranylgeranyltransferase activity 1.24e-08 7.99e-06 protein geranylgeranylation 3.63e-08 1.50e-05 Rab guanyl-nucleotide exchange factor activity 6.56e-08 2.32e-05 recycling endosome 9.47e-08 5.37e-05 negative regulation of adiponectin secretion 1.11e-07 4.24e-05 protein farnesyltransferase activity 2.87e-07 1.01e-04 Rab geranylgeranyltransferase activity 3.72e-07 1.17e-04 protein farnesyltransferase complex 4.36e-07 2.21e-04 protein farnesylation 1.61e-06 7.36e-04 hormone secretion 2.90e-06 1.26e-03 endomembrane system organization 4.16e-06 1.09e-03 endosome 5.15e-06 2.13e-03 regulation of secretion

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 5.03e-03 4.13e-01 APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS 5.23e-03 4.74e-01 REGULATION OF WATER BALANCE BY RENAL AQUAPORINS 1.17e-02 8.35e-01 REGULATION OF WATER BALANCE BY RENAL AQUAPORINS 1.53e-02 1.00e+00 APOPTOTIC EXECUTION PHASE 1.54e-02 1.00e+00 AQUAPORIN MEDIATED TRANSPORT 1.57e-02 1.00e+00 MITOTIC M M G1 PHASES 1.92e-02 1.00e+00 DNA REPLICATION 1.94e-02 1.00e+00 TOLL RECEPTOR CASCADES 1.96e-02 1.00e+00 TOLL RECEPTOR CASCADES 2.21e-02 1.00e+00 APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS 3.08e-02 1.00e+00 MITOTIC M M G1 PHASES 3.08e-02 1.00e+00 AQUAPORIN MEDIATED TRANSPORT 3.09e-02 1.00e+00 DNA REPLICATION 3.21e-02 1.00e+00 APOPTOTIC EXECUTION PHASE 4.13e-02 1.00e+00 APOPTOSIS 4.30e-02 1.00e+00 CELL CYCLE MITOTIC

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.97e-03 1e+00 abnormal synaptic vesicle number 3.59e-03 1e+00 decreased oxygen consumption 5.61e-03 1e+00 absent liver 5.61e-03 1e+00 abnormal interscapular fat pad morphology 7.48e-03 1e+00 abnormal histamine physiology 7.48e-03 1e+00 abnormal cochlear IHC efferent innervation pattern 9.34e-03 1e+00 abnormal cochlear outer hair cell physiology 9.34e-03 1e+00 abnormal cochlear OHC efferent innervation pattern 9.34e-03 1e+00 abnormal cochlear hair cell physiology 1.12e-02 1e+00 increased mast cell number 1.12e-02 1e+00 abnormal cochlear inner hair cell physiology 1.12e-02 1e+00 abnormal liver bud morphology 1.12e-02 1e+00 thin placenta labyrinth 1.12e-02 1e+00 abnormal mesenteric fat pad morphology 1.12e-02 1e+00 absent acrosome 1.31e-02 1e+00 delayed hepatic development 1.31e-02 1e+00 abnormal gas homeostasis 1.44e-02 1e+00 increased circulating triglyceride level 1.68e-02 1e+00 abnormal pituitary gland development 1.86e-02 1e+00 umbilical hernia

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

²FDR corrected p-value (Benjamini-Hochberg)