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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod210

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod210 Module size 40 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10566 AKAP3 A-kinase anchoring protein 3 57821 C1orf114 coiled-coil domain containing 181 128602 C20orf85 chromosome 20 open reading frame 85 129852 C2orf73 chromosome 2 open reading frame 73 57820 CCNB1IP1 cyclin B1 interacting protein 1 25792 CIZ1 CDKN1A interacting zinc finger protein 1 1365 CLDN3 claudin 3 1366 CLDN7 claudin 7 285093 CXXC11 receptor transporter protein 5 (putative) 51705 EMCN endomucin 2013 EMP2 epithelial membrane protein 2 4072 EPCAM epithelial cell adhesion molecule 9852 EPM2AIP1 EPM2A interacting protein 1 2697 GJA1 gap junction protein alpha 1 10223 GPA33 glycoprotein A33 286676 ILDR1 immunoglobulin like domain containing receptor 1 85379 KIAA1671 KIAA1671 84708 MPDZ ligand of numb-protein X 1 10205 MPZL2 myelin protein zero like 2 196264 MPZL3 myelin protein zero like 3 59338 PLEKHA1 pleckstrin homology domain containing A1 59339 PLEKHA2 pleckstrin homology domain containing A2 83483 PLVAP plasmalemma vesicle associated protein 78994 PRR14 proline rich 14 54538 ROBO4 roundabout guidance receptor 4 54763 ROPN1 rhophilin associated tail protein 1 152015 ROPN1B rhophilin associated tail protein 1B 83853 ROPN1L rhophilin associated tail protein 1 like 83861 RSPH3 radial spoke head 3 homolog 53340 SPA17 sperm autoantigenic protein 17 4070 TACSTD2 tumor associated calcium signal transducer 2 6975 TECTB tectorin beta 51368 TEX264 testis expressed 264 7082 TJP1 tight junction protein 1 9414 TJP2 tight junction protein 2 55273 TMEM100 transmembrane protein 100 84283 TMEM79 transmembrane protein 79 64102 TNMD tenomodulin 10099 TSPAN3 tetraspanin 3 150165 XKR3 XK related 3

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 1.64e-01 1.69e-03 Reactome Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane Vesicle-mediated transport 1.49e-01 8.25e-06 Reactome c-src mediated regulation of Cx43 function and closure of gap junctions Vesicle-mediated transport 1.43e-01 8.25e-06 Reactome Regulation of gap junction activity Vesicle-mediated transport 3.09e-02 4.12e-06 GO apicolateral plasma membrane cellular_component 1.81e-02 7.49e-06 GO sperm capacitation biological_process 4.75e-03 3.76e-08 GO lateral plasma membrane cellular_component 4.54e-03 2.12e-04 GO epithelial cilium movement biological_process 2.77e-03 1.11e-09 GO bicellular tight junction cellular_component

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 1.37e-07 4.55e-05 bicellular tight junction 3.54e-07 1.12e-04 apical junction complex 7.62e-07 3.71e-04 endothelium development 2.59e-06 7.07e-04 cell-cell junction 8.87e-06 2.20e-03 lateral plasma membrane 1.29e-05 4.87e-03 endothelial cell differentiation 1.30e-05 4.90e-03 epithelial cell development 1.46e-05 3.46e-03 apicolateral plasma membrane 2.89e-05 6.90e-03 PDZ domain binding 4.07e-05 9.41e-03 cell adhesion molecule binding 1.30e-04 3.65e-02 endothelial cell development 1.61e-04 4.37e-02 cell-cell adhesion 2.13e-04 3.80e-02 motile cilium 2.22e-04 3.95e-02 sperm fibrous sheath 2.65e-04 6.65e-02 epithelial cell differentiation 2.81e-04 6.97e-02 establishment of endothelial intestinal barrier 3.33e-04 8.02e-02 regulation of glomerular filtration 4.31e-04 9.91e-02 acrosome reaction 4.89e-04 1.10e-01 regulation of vasculogenesis 5.41e-04 8.63e-02 sperm principal piece

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.01e-05 5.28e-03 APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS 4.47e-05 6.03e-03 SIGNALING BY HIPPO 3.69e-04 4.92e-02 APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS 4.31e-04 5.65e-02 SIGNALING BY HIPPO 4.67e-04 5.10e-02 APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS 5.67e-04 7.20e-02 APOPTOTIC EXECUTION PHASE 1.43e-03 1.60e-01 TIGHT JUNCTION INTERACTIONS 1.72e-03 1.87e-01 GAP JUNCTION ASSEMBLY 2.22e-03 2.04e-01 APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS 2.25e-03 2.06e-01 APOPTOTIC EXECUTION PHASE 2.39e-03 2.49e-01 APOPTOSIS 3.11e-03 3.10e-01 CELL CELL JUNCTION ORGANIZATION 3.42e-03 3.35e-01 MEMBRANE TRAFFICKING 3.87e-03 3.30e-01 MEMBRANE TRAFFICKING 4.53e-03 4.21e-01 CELL JUNCTION ORGANIZATION 4.84e-03 4.00e-01 GAP JUNCTION DEGRADATION 5.35e-03 4.34e-01 APOPTOSIS 5.39e-03 4.37e-01 TIGHT JUNCTION INTERACTIONS 6.39e-03 5.59e-01 CELL CELL COMMUNICATION 1.03e-02 8.15e-01 GAP JUNCTION DEGRADATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.82e-04 4.35e-01 intestinal edema 3.53e-04 4.92e-01 abnormal spermatocyte morphology 3.67e-04 5.05e-01 impaired skin barrier function 5.32e-04 6.31e-01 abnormal developmental vascular remodeling 5.82e-04 6.64e-01 brittle hair 6.62e-04 7.16e-01 abnormal trabecula carnea morphology 2.59e-03 1.00e+00 abnormal intestine physiology 3.76e-03 1.00e+00 abnormal pulmonary endothelial cell surface 4.34e-03 1.00e+00 abnormal epidermis stratum corneum morphology 5.63e-03 1.00e+00 interparietal bone hypoplasia 5.88e-03 1.00e+00 abnormal coat appearance 6.25e-03 1.00e+00 abnormal skin condition 7.49e-03 1.00e+00 increased behavioral withdrawal response 7.49e-03 1.00e+00 abnormal heart layer morphology 7.52e-03 1.00e+00 patent foramen ovale 9.35e-03 1.00e+00 semilunar valve regurgitation 9.35e-03 1.00e+00 abnormal dermis reticular layer morphology 9.36e-03 1.00e+00 abnormal heart right ventricle outflow tract morphology 9.37e-03 1.00e+00 small nasal bone 9.62e-03 1.00e+00 dermatitis

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

²FDR corrected p-value (Benjamini-Hochberg)