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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod357

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod357 Module size 65 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 88455 ANKRD13A ankyrin repeat domain 13A 23568 ARL2BP ADP ribosylation factor like GTPase 2 binding protein 348110 C15orf38 actin related protein 2/3 complex inhibitor 79173 C19orf57 chromosome 19 open reading frame 57 130951 C2orf65 meiosis 1 associated protein 79669 C3orf52 chromosome 3 open reading frame 52 201725 C4orf46 chromosome 4 open reading frame 46 11094 CACFD1 calcium channel flower domain containing 1 64770 CCDC14 coiled-coil domain containing 14 910 CD1B CD1b molecule 970 CD70 CD70 molecule 56990 CDC42SE2 CDC42 small effector 2 23274 CLEC16A C-type lectin domain containing 16A 387836 CLEC2A C-type lectin domain family 2 member A 54918 CMTM6 CKLF like MARVEL transmembrane domain containing 6 54939 COMMD4 COMM domain containing 4 28991 COMMD5 COMM domain containing 5 1362 CPD carboxypeptidase D 93099 DMKN dermokine 91748 ELMSAN1 ELM2 and Myb/SANT domain containing 1 79607 FAM118B family with sequence similarity 118 member B 8933 FAM127A retrotransposon Gag like 8C 441518 FAM127C retrotransposon Gag like 8B 162427 FAM134C reticulophagy regulator family member 3 23272 FAM208A family with sequence similarity 208 member A 27145 FILIP1 filamin A interacting protein 1 729408 GAGE2D G antigen 2D 168537 GIMAP7 GTPase, IMAP family member 7 64207 IRF2BPL interferon regulatory factor 2 binding protein like 57179 KIAA1191 KIAA1191 22998 LIMCH1 LIM and calponin homology domains 1 25840 METTL7A methyltransferase like 7A 57509 MTUS1 microtubule associated scaffold protein 1 133686 NADKD1 NAD kinase 2, mitochondrial 387921 NHLRC3 NHL repeat containing 3 10360 NPM3 nucleophosmin/nucleoplasmin 3 54956 PARP16 poly(ADP-ribose) polymerase family member 16 5082 PDCL phosducin like 118987 PDZD8 PDZ domain containing 8 65979 PHACTR4 phosphatase and actin regulator 4 84295 PHF6 PHD finger protein 6 9581 PREPL prolyl endopeptidase like 221749 PXDC1 PX domain containing 1 221687 RNF182 ring finger protein 182 57674 RNF213 ring finger protein 213 257160 RNF214 ring finger protein 214 54665 RSBN1 round spermatid basic protein 1 51435 SCARA3 scavenger receptor class A member 3 6398 SECTM1 secreted and transmembrane 1 57619 SHROOM3 shroom family member 3 9122 SLC16A4 solute carrier family 16 member 4 10560 SLC19A2 solute carrier family 19 member 2 6698 SPRR1A small proline rich protein 1A 79953 SYNDIG1 synapse differentiation inducing 1 80731 THSD7B thrombospondin type 1 domain containing 7B 497189 TIFAB TIFA inhibitor 83941 TM2D1 TM2 domain containing 1 126282 TNFAIP8L1 TNF alpha induced protein 8 like 1 84629 TNRC18 trinucleotide repeat containing 18 10194 TSHZ1 teashirt zinc finger homeobox 1 57616 TSHZ3 teashirt zinc finger homeobox 3 10078 TSSC4 tumor suppressing subtransferable candidate 4 9816 URB2 URB2 ribosome biogenesis homolog 84460 ZMAT1 zinc finger matrin-type 1 64397 ZNF474 zinc finger protein 106

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).

No specific annotations were found for this module

All enriched annotations

Gene Ontology

P-value1 FDR2 Term 1.37e-04 2.71e-02 serine-type exopeptidase activity 1.83e-04 4.86e-02 neural tube closure 3.59e-04 8.55e-02 neural tube formation 4.69e-04 1.06e-01 embryonic epithelial tube formation 5.31e-04 1.18e-01 morphogenesis of embryonic epithelium 6.61e-04 1.41e-01 epithelial tube formation 7.33e-04 1.53e-01 tube formation 1.41e-03 2.08e-01 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding 1.74e-03 3.09e-01 neural tube development 1.95e-03 3.34e-01 embryonic camera-type eye formation 1.95e-03 3.34e-01 optic cup morphogenesis involved in camera-type eye development 1.95e-03 3.34e-01 positive regulation of nuclease activity 1.95e-03 3.34e-01 activation of signaling protein activity involved in unfolded protein response 2.01e-03 3.42e-01 epithelial tube morphogenesis 2.66e-03 4.29e-01 tube morphogenesis 3.90e-03 5.71e-01 embryonic camera-type eye morphogenesis 3.90e-03 5.71e-01 soft palate development 3.90e-03 5.71e-01 protein auto-ADP-ribosylation 4.74e-03 6.66e-01 apoptotic signaling pathway 5.17e-03 7.13e-01 embryonic morphogenesis

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.82e-02 1e+00 GOLGI ASSOCIATED VESICLE BIOGENESIS 1.92e-02 1e+00 TRANS GOLGI NETWORK VESICLE BUDDING 2.16e-02 1e+00 GOLGI ASSOCIATED VESICLE BIOGENESIS 2.58e-02 1e+00 TRANS GOLGI NETWORK VESICLE BUDDING 4.92e-02 1e+00 MEMBRANE TRAFFICKING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 9.59e-04 8.83e-01 wavy neural tube 5.61e-03 1.00e+00 abnormal ureter smooth muscle morphology 5.61e-03 1.00e+00 impaired ureteric peristalsis 5.61e-03 1.00e+00 absent malleus processus brevis 5.61e-03 1.00e+00 gonial bone hypoplasia 5.61e-03 1.00e+00 abnormal epiglottis morphology 5.61e-03 1.00e+00 decreased cervical vertebrae number 5.62e-03 1.00e+00 abnormal malleus morphology 7.47e-03 1.00e+00 absent neurocranium 7.48e-03 1.00e+00 abnormal external auditory canal morphology 7.50e-03 1.00e+00 abnormal xiphoid process morphology 7.57e-03 1.00e+00 wavy tail 7.75e-03 1.00e+00 impaired hearing 9.33e-03 1.00e+00 increased sternebra number 1.12e-02 1.00e+00 abnormal soft palate morphology 1.12e-02 1.00e+00 abnormal olfactory bulb granule cell layer morphology 1.12e-02 1.00e+00 herniated intestine 1.13e-02 1.00e+00 decreased hemoglobin content 1.30e-02 1.00e+00 dilated ureter 1.30e-02 1.00e+00 abnormal ureter development

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

²FDR corrected p-value (Benjamini-Hochberg)