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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod237

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod237 Module size 72 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 56271 BEX4 brain expressed X-linked 4 140707 BRI3BP BRI3 binding protein 55727 BTBD7 BTB domain containing 7 55088 C10orf118 coiled-coil domain containing 186 728568 C12orf73 chromosome 12 open reading frame 73 100526783 C15orf38-AP3S2 C15orf38-AP3S2 readthrough 8209 C21orf33 glutamine amidotransferase like class 1 domain containing 3A 646603 C4orf51 chromosome 4 open reading frame 51 203111 C8orf47 glutamate rich 5 642475 C8orf73 maestro heat like repeat family member 6 286257 C9orf142 PAXX, non-homologous end joining factor 23261 CAMTA1 calmodulin binding transcription activator 1 339230 CCDC137 coiled-coil domain containing 137 9720 CCDC144A coiled-coil domain containing 144A 80071 CCDC15 coiled-coil domain containing 15 100526761 CCDC169-SOHLH2 CCDC169-SOHLH2 readthrough 9236 CCPG1 cell cycle progression 1 100142659 CTAGE8 CTAGE family member 8 54465 ETAA1 ETAA1, ATR kinase activator 159091 FAM122C family with sequence similarity 122C 63877 FAM204A family with sequence similarity 204 member A 145773 FAM81A family with sequence similarity 81 member A 157769 FAM91A1 family with sequence similarity 91 member A1 729438 GATSL2 cytosolic arginine sensor for mTORC1 subunit 2 116254 GINM1 glycoprotein integral membrane 1 83468 GLT8D2 glycosyltransferase 8 domain containing 2 653073 GOLGA8J golgin A8 family member J 57493 HEG1 heart development protein with EGF like domains 1 219844 HYLS1 HYLS1, centriolar and ciliogenesis associated 389792 IER5L immediate early response 5 like 23351 KHNYN KH and NYN domain containing 57613 KIAA1467 family with sequence similarity 234 member B 144501 KRT80 keratin 80 85329 LGALS12 galectin 12 151963 MB21D2 Mab-21 domain containing 2 27136 MORC1 MORC family CW-type zinc finger 1 56180 MOSPD1 motile sperm domain containing 1 55686 MREG melanoregulin 26579 MYEOV myeloma overexpressed 284565 NBPF16 NBPF member 15 57489 ODF2L outer dense fiber of sperm tails 2 like 161725 OTUD7A OTU deubiquitinase 7A 148479 PHF13 PHD finger protein 13 55344 PLCXD1 phosphatidylinositol specific phospholipase C X domain containing 1 257068 PLCXD2 phosphatidylinositol specific phospholipase C X domain containing 2 80301 PLEKHO2 pleckstrin homology domain containing O2 57460 PPM1H protein phosphatase, Mg2+/Mn2+ dependent 1H 84279 PRADC1 protease associated domain containing 1 343071 PRAMEF10 PRAME family member 10 440561 PRAMEF6 PRAME family member 6 389151 PRR23B proline rich 23B 389362 PSMG4 proteasome assembly chaperone 4 9827 RGP1 RGP1 homolog, RAB6A GEF complex partner 1 440400 RNASEK ribonuclease K 79634 SCRN3 secernin 3 148641 SLC35F3 solute carrier family 35 member F3 139065 SLITRK4 SLIT and NTRK like family member 4 389763 SPATA31D1 SPATA31 subfamily D member 1 80208 SPG11 SPG11, spatacsin vesicle trafficking associated 64420 SUSD1 sushi domain containing 1 116238 TLCD1 TLC domain containing 1 51768 TM7SF3 transmembrane 7 superfamily member 3 54664 TMEM106B transmembrane protein 106B 124491 TMEM170A transmembrane protein 170A 79134 TMEM185B transmembrane protein 185B 55248 TMEM206 transmembrane protein 206 55254 TMEM39A transmembrane protein 39A 55076 TMEM45A transmembrane protein 45A 25941 TPGS2 tubulin polyglutamylase complex subunit 2 10906 TRAFD1 TRAF-type zinc finger domain containing 1 54877 ZCCHC2 zinc finger CCHC-type containing 2 440590 ZYG11A zyg-11 family member A, cell cycle regulator

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 3.04e-02 2.01e-04 GO phosphoric diester hydrolase activity molecular_function

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 5.92e-04 1.28e-01 cell morphogenesis involved in differentiation 1.45e-03 2.67e-01 cell morphogenesis 1.95e-03 3.34e-01 positive regulation of fibroblast growth factor production 2.13e-03 3.58e-01 lysosome organization 2.40e-03 3.30e-01 phosphoric diester hydrolase activity 3.02e-03 4.75e-01 cell morphogenesis involved in neuron differentiation 3.90e-03 5.71e-01 regulation of branching involved in salivary gland morphogenesis 3.90e-03 5.71e-01 DNA hypermethylation 4.06e-03 5.89e-01 neuron projection morphogenesis 4.34e-03 4.94e-01 Ku70:Ku80 complex 4.64e-03 6.55e-01 cell projection morphogenesis 4.86e-03 5.99e-01 lactose binding 4.86e-03 5.99e-01 arginine binding 4.96e-03 6.09e-01 phosphoric ester hydrolase activity 5.19e-03 6.31e-01 protein serine/threonine kinase activator activity 5.62e-03 7.63e-01 cell part morphogenesis 5.84e-03 7.72e-01 venous blood vessel morphogenesis 5.84e-03 7.72e-01 ventricular trabecula myocardium morphogenesis 5.84e-03 7.72e-01 endothelial cell morphogenesis 5.84e-03 7.72e-01 negative regulation of DNA-templated transcription, initiation

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 7.33e-04 7.56e-01 testicular atrophy 1.63e-03 1.00e+00 small testis 1.73e-03 1.00e+00 increased sacral vertebrae number 1.74e-03 1.00e+00 decreased lumbar vertebrae number 3.74e-03 1.00e+00 abnormal lymphatic vessel endothelium morphology 4.02e-03 1.00e+00 decreased male germ cell number 5.61e-03 1.00e+00 decreased primary ovarian follicle number 5.61e-03 1.00e+00 impaired granulosa cell differentiation 5.61e-03 1.00e+00 abnormal free fatty acids level 5.62e-03 1.00e+00 abnormal hormone level 7.48e-03 1.00e+00 chylous ascites 7.55e-03 1.00e+00 partial lethality throughout fetal growth and development 9.37e-03 1.00e+00 lymphangiectasis 1.12e-02 1.00e+00 abnormal oogenesis 1.12e-02 1.00e+00 ovary atrophy 1.12e-02 1.00e+00 increased glycerol level 1.12e-02 1.00e+00 abnormal survival 1.31e-02 1.00e+00 abnormal lymph circulation 1.35e-02 1.00e+00 partial embryonic lethality during organogenesis 1.49e-02 1.00e+00 decreased inguinal fat pad weight

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

²FDR corrected p-value (Benjamini-Hochberg)