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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod228

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod228 Module size 62 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 79719 AAGAB alpha and gamma adaptin binding protein 3268 AGFG2 ArfGAP with FG repeats 2 273 AMPH amphiphysin 161 AP2A2 adaptor related protein complex 2 subunit alpha 2 23080 AVL9 AVL9 cell migration associated 274 BIN1 bridging integrator 1 51411 BIN2 bridging integrator 2 283152 CCDC153 coiled-coil domain containing 153 972 CD74 CD74 molecule 66005 CHID1 chitinase domain containing 1 130162 CLHC1 clathrin heavy chain linker domain containing 1 1213 CLTC clathrin heavy chain 8218 CLTCL1 clathrin heavy chain like 1 1486 CTBS chitobiase 404093 CUEDC1 CUE domain containing 1 1601 DAB2 DAB2, clathrin adaptor protein 57706 DENND1A DENN domain containing 1A 163486 DENND1B DENN domain containing 1B 79958 DENND1C DENN domain containing 1C 27147 DENND2A DENN domain containing 2A 163259 DENND2C DENN domain containing 2C 79961 DENND2D DENN domain containing 2D 1759 DNM1 dynamin 1 1785 DNM2 dynamin 2 25975 EGFL6 EGF like domain multiple 6 30846 EHD2 EH domain containing 2 150350 ENTHD1 ENTH domain containing 1 29924 EPN1 epsin 1 22905 EPN2 epsin 2 55040 EPN3 epsin 3 2060 EPS15 epidermal growth factor receptor pathway substrate 15 58513 EPS15L1 epidermal growth factor receptor pathway substrate 15 like 1 89848 FCHSD1 FCH and double SH3 domains 1 23048 FNBP1 formin binding protein 1 2495 FTH1 ferritin heavy chain 1 2512 FTL ferritin light chain 23015 GOLGA8A golgin A8 family member A 124790 HEXIM2 hexamethylene bisacetamide inducible 2 9146 HGS hepatocyte growth factor-regulated tyrosine kinase substrate 50618 ITSN2 intersectin 2 3883 KRT33A keratin 33A 55323 LARP6 La ribonucleoprotein domain family member 6 5641 LGMN legumain 4074 M6PR mannose-6-phosphate receptor, cation dependent 79694 MANEA mannosidase endo-alpha 84179 MFSD7 solute carrier family 49 member 3 51172 NAGPA N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase 55690 PACS1 phosphofurin acidic cluster sorting protein 1 10630 PDPN podoplanin 8301 PICALM phosphatidylinositol binding clathrin assembly protein 729359 PLIN4 perilipin 4 768239 PSAPL1 prosaposin like 1 (gene/pseudogene) 85021 REPS1 RALBP1 associated Eps domain containing 1 9185 REPS2 RALBP1 associated Eps domain containing 2 152503 SH3D19 SH3 domain containing 19 6456 SH3GL2 SH3 domain containing GRB2 like 2, endophilin A1 51429 SNX9 sorting nexin 9 6764 ST5 suppression of tumorigenicity 5 23166 STAB1 stabilin 1 23336 SYNM synemin 10043 TOM1 target of myb1 membrane trafficking protein 10040 TOM1L1 target of myb1 like 1 membrane trafficking protein

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 2.34e-01 3.83e-11 Reactome Formation of annular gap junctions Vesicle-mediated transport 1.02e-01 2.72e-06 GO phosphatidylinositol phosphate binding molecular_function 5.29e-02 6.01e-10 Reactome Retrograde neurotrophin signalling Signal Transduction 4.57e-02 2.85e-08 GO endocytic recycling biological_process 4.49e-02 1.35e-30 Reactome Clathrin-mediated endocytosis Vesicle-mediated transport 4.40e-02 2.72e-06 GO clathrin light chain binding molecular_function 4.26e-02 2.75e-10 GO Rab guanyl-nucleotide exchange factor activity molecular_function 3.61e-02 3.70e-04 GO ferroxidase activity molecular_function 3.17e-02 9.42e-20 GO endocytosis biological_process 2.55e-02 7.01e-14 GO clathrin-coated pit cellular_component 2.50e-02 2.29e-27 GO membrane organization biological_process 2.50e-02 2.85e-08 GO negative regulation of epidermal growth factor receptor signaling pathway biological_process 1.69e-02 2.00e-13 GO clathrin-coated vesicle cellular_component 1.62e-02 1.24e-08 Reactome EGFR downregulation Signal Transduction 1.45e-02 4.62e-04 GO autolysosome cellular_component 1.14e-02 2.67e-14 Reactome Clathrin derived vesicle budding Vesicle-mediated transport 1.05e-02 2.67e-14 Reactome trans-Golgi Network Vesicle Budding Vesicle-mediated transport 7.02e-03 4.62e-04 GO negative regulation of vascular endothelial growth factor receptor signaling pathway biological_process 4.78e-03 1.45e-05 GO plasma membrane tubulation biological_process 7.07e-04 7.64e-11 Reactome Gap junction degradation Vesicle-mediated transport 4.70e-04 3.88e-06 GO clathrin complex 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 0.00e+00 0.00e+00 endosomal transport 0.00e+00 0.00e+00 endocytosis 0.00e+00 0.00e+00 receptor-mediated endocytosis 0.00e+00 0.00e+00 clathrin-coated vesicle 0.00e+00 0.00e+00 clathrin-coated pit 8.05e-10 3.67e-07 coated vesicle 5.17e-09 2.46e-06 Rab guanyl-nucleotide exchange factor activity 2.69e-08 1.66e-05 negative regulation of ERBB signaling pathway 9.35e-08 3.61e-05 clathrin binding 1.10e-07 3.74e-05 clathrin-coated vesicle membrane 2.22e-07 1.18e-04 negative regulation of epidermal growth factor receptor signaling pathway 3.00e-07 1.57e-04 clathrin-dependent endocytosis 3.97e-07 2.03e-04 regulation of ERBB signaling pathway 4.46e-07 2.26e-04 iron ion transport 7.39e-07 3.61e-04 endocytic recycling 1.04e-06 4.92e-04 antigen processing and presentation of exogenous peptide antigen via MHC class II 1.12e-06 5.27e-04 antigen processing and presentation of peptide antigen via MHC class II 1.12e-06 5.27e-04 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 1.16e-06 3.36e-04 clathrin vesicle coat 1.34e-06 3.85e-04 clathrin-coated endocytic vesicle

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 TRANS GOLGI NETWORK VESICLE BUDDING 0.00e+00 0.00e+00 MEMBRANE TRAFFICKING 0.00e+00 0.00e+00 TRANS GOLGI NETWORK VESICLE BUDDING 0.00e+00 0.00e+00 MEMBRANE TRAFFICKING 1.64e-11 6.26e-09 GOLGI ASSOCIATED VESICLE BIOGENESIS 3.54e-11 1.01e-08 GOLGI ASSOCIATED VESICLE BIOGENESIS 8.51e-11 3.10e-08 EGFR DOWNREGULATION 8.86e-11 2.43e-08 EGFR DOWNREGULATION 1.77e-09 5.66e-07 GAP JUNCTION DEGRADATION 2.12e-09 4.96e-07 GAP JUNCTION DEGRADATION 2.60e-08 5.46e-06 RETROGRADE NEUROTROPHIN SIGNALLING 3.04e-08 8.41e-06 RETROGRADE NEUROTROPHIN SIGNALLING 6.01e-08 1.20e-05 MHC CLASS II ANTIGEN PRESENTATION 8.06e-08 2.10e-05 MHC CLASS II ANTIGEN PRESENTATION 2.26e-07 5.60e-05 GAP JUNCTION TRAFFICKING 3.06e-07 5.67e-05 GAP JUNCTION TRAFFICKING 4.05e-07 9.66e-05 RECYCLING PATHWAY OF L1 6.90e-07 1.23e-04 RECYCLING PATHWAY OF L1 2.72e-06 4.42e-04 LYSOSOME VESICLE BIOGENESIS 2.93e-06 6.09e-04 LYSOSOME VESICLE BIOGENESIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.75e-05 1.74e-01 increased lysosomal enzyme secretion 4.09e-04 5.37e-01 decreased mean corpuscular hemoglobin 5.44e-04 6.39e-01 lysosomal protein accumulation 8.08e-04 7.96e-01 abnormal synaptic vesicle recycling 1.31e-03 1.00e+00 tonic seizures 3.98e-03 1.00e+00 decreased mean corpuscular hemoglobin concentration 4.26e-03 1.00e+00 abnormal iron homeostasis 4.28e-03 1.00e+00 abnormal cell physiology 4.51e-03 1.00e+00 abnormal proximal convoluted tubule morphology 4.51e-03 1.00e+00 abnormal spleen B cell follicle morphology 5.62e-03 1.00e+00 abnormal visceral yolk sac cavity morphology 6.44e-03 1.00e+00 muscular atrophy 7.49e-03 1.00e+00 increased transitional stage T1 B cell number 7.49e-03 1.00e+00 abnormal spinal cord grey matter morphology 9.35e-03 1.00e+00 small proamniotic cavity 9.37e-03 1.00e+00 opisthotonus 9.39e-03 1.00e+00 absent foregut 1.07e-02 1.00e+00 complete embryonic lethality 1.12e-02 1.00e+00 abnormal marginal zone B cell morphology 1.12e-02 1.00e+00 ventricular cardiomyopathy

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

²FDR corrected p-value (Benjamini-Hochberg)