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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod370

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod370 Module size 68 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 177 AGER advanced glycosylation end-product specific receptor 55966 AJAP1 adherens junctions associated protein 1 240 ALOX5 arachidonate 5-lipoxygenase 84168 ANTXR1 ANTXR cell adhesion molecule 1 302 ANXA2 annexin A2 8416 ANXA9 annexin A9 322 APBB1 amyloid beta precursor protein binding family B member 1 323 APBB2 amyloid beta precursor protein binding family B member 2 10307 APBB3 amyloid beta precursor protein binding family B member 3 408 ARRB1 arrestin beta 1 575 BAI1 adhesion G protein-coupled receptor B1 57596 BEGAIN brain enriched guanylate kinase associated 339210 C17orf67 chromosome 17 open reading frame 67 57124 CD248 CD248 molecule 947 CD34 CD34 molecule 9308 CD83 CD83 molecule 9859 CEP170 centrosomal protein 170 10164 CHST4 carbohydrate sulfotransferase 4 1775 DNASE1L2 deoxyribonuclease 1 like 2 8448 DOC2A double C2 domain alpha 1896 EDA ectodysplasin A 2037 EPB41L2 erythrocyte membrane protein band 4.1 like 2 2107 ERF eukaryotic translation termination factor 1 64919 GBP3 B cell CLL/lymphoma 11B 2670 GFAP glial fibrillary acidic protein 22997 IGSF9B immunoglobulin superfamily member 9B 27189 IL17C interleukin 17C 23765 IL17RA interleukin 17 receptor A 84818 IL17RC interleukin 17 receptor C 132014 IL17RE interleukin 17 receptor E 10068 IL18BP interleukin 18 binding protein 56005 IL25 myeloid derived growth factor 27178 IL37 interleukin 37 100505385 IQCJ-SCHIP1 IQCJ-SCHIP1 readthrough 889 KRIT1 KRIT1, ankyrin repeat containing 29124 LGALS13 galectin 13 9863 MAGI2 membrane associated guanylate kinase, WW and PDZ domain containing 2 55777 MBD5 methyl-CpG binding domain protein 5 4162 MCAM melanoma cell adhesion molecule 4684 NCAM1 neural cell adhesion molecule 1 259197 NCR3 natural cytotoxicity triggering receptor 3 8390 OR1G1 olfactory receptor family 1 subfamily G member 1 5047 PAEP progestagen associated endometrial protein 54103 PION gamma-secretase activating protein 22874 PLEKHA6 pleckstrin homology domain containing A6 5493 PPL periplakin 8842 PROM1 prominin 1 79056 PRRG4 proline rich and Gla domain 4 85376 RIMBP3 RIMS binding protein 3 10069 RWDD2B RWD domain containing 2B 6285 S100B S100 calcium binding protein B 6286 S100P S100 calcium binding protein P 170591 S100Z S100 calcium binding protein Z 10648 SCGB1D1 secretoglobin family 1D member 1 6401 SELE selectin E 9351 SLC9A3R2 SLC9A3 regulator 2 6622 SNCA synuclein alpha 22986 SORCS3 sortilin related VPS10 domain containing receptor 3 6272 SORT1 sortilin 1 6656 SOX1 SRY-box 1 6693 SPN sialophorin 79933 SYNPO2L synaptopodin 2 like 80835 TAS1R1 taste 1 receptor member 1 26136 TES testin LIM domain protein 7031 TFF1 trefoil factor 1 79865 TREML2 triggering receptor expressed on myeloid cells like 2 83889 WDR87 WD repeat domain 87 8840 WISP1 WNT1 inducible signaling pathway protein 1

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 2.04e-01 3.38e-03 GO arachidonate 5-lipoxygenase activity molecular_function 1.78e-01 3.38e-03 Reactome Biosynthesis of DPAn-3-derived 13-series resolvins Metabolism 8.18e-02 1.11e-04 Reactome Interleukin-18 signaling Immune System 5.53e-02 1.62e-05 GO S100 protein binding molecular_function 3.45e-02 2.88e-05 GO tau protein binding molecular_function 2.49e-02 1.01e-02 Reactome NFG and proNGF binds to p75NTR Signal Transduction 2.01e-02 6.04e-04 GO glomerular filtration biological_process 1.68e-02 6.17e-05 GO positive regulation of receptor internalization biological_process 1.25e-02 6.04e-04 GO RAGE receptor binding molecular_function 7.64e-03 7.24e-04 GO nerve growth factor signaling pathway biological_process 5.68e-03 3.77e-06 Reactome Interleukin-17 signaling Immune System

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 6.71e-06 1.81e-03 interleukin-17 receptor activity 8.26e-06 2.19e-03 tau protein binding 1.35e-05 3.43e-03 S100 protein binding 6.48e-05 2.01e-02 positive regulation of receptor-mediated endocytosis 6.50e-05 1.35e-02 cell surface 8.47e-05 2.53e-02 inflammatory response 1.13e-04 3.24e-02 vascular wound healing 1.55e-04 4.23e-02 positive regulation of receptor internalization 2.03e-04 5.31e-02 positive regulation of endocytosis 2.27e-04 5.83e-02 positive regulation of interleukin-13 secretion 2.70e-04 4.93e-02 beta-amyloid binding 3.70e-04 8.75e-02 positive regulation of protein secretion 3.94e-04 6.83e-02 calcium-dependent phospholipid binding 4.35e-04 7.44e-02 calcium ion binding 4.65e-04 1.05e-01 regulation of receptor-mediated endocytosis 5.37e-04 1.19e-01 response to iron ion 5.41e-04 1.19e-01 regulation of receptor internalization 5.50e-04 1.21e-01 glomerular filtration 5.72e-04 1.25e-01 positive regulation of peptide secretion 5.98e-04 9.36e-02 external side of plasma membrane

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 4.90e-04 5.33e-02 ADVANCED GLYCOSYLATION ENDPRODUCT RECEPTOR SIGNALING 7.91e-04 9.58e-02 RIP MEDIATED NFKB ACTIVATION VIA DAI 8.04e-04 9.72e-02 ADVANCED GLYCOSYLATION ENDPRODUCT RECEPTOR SIGNALING 9.74e-04 1.15e-01 TRAF6 MEDIATED NFKB ACTIVATION 1.48e-03 1.42e-01 RIP MEDIATED NFKB ACTIVATION VIA DAI 1.63e-03 1.79e-01 TAK1 ACTIVATES NFKB BY PHOSPHORYLATION AND ACTIVATION OF IKKS COMPLEX 2.19e-03 2.02e-01 TRAF6 MEDIATED NFKB ACTIVATION 2.75e-03 2.46e-01 GOLGI ASSOCIATED VESICLE BIOGENESIS 2.89e-03 2.57e-01 TAK1 ACTIVATES NFKB BY PHOSPHORYLATION AND ACTIVATION OF IKKS COMPLEX 3.80e-03 3.25e-01 TRANS GOLGI NETWORK VESICLE BUDDING 4.49e-03 3.75e-01 NUCLEAR SIGNALING BY ERBB4 4.55e-03 4.22e-01 NUCLEAR SIGNALING BY ERBB4 8.20e-03 6.85e-01 GOLGI ASSOCIATED VESICLE BIOGENESIS 9.83e-03 7.91e-01 TRANS GOLGI NETWORK VESICLE BUDDING 1.19e-02 9.15e-01 TRAF6 MEDIATED INDUCTION OF NFKB AND MAP KINASES UPON TLR7 8 OR 9 ACTIVATION 1.24e-02 9.44e-01 NFKB AND MAP KINASES ACTIVATION MEDIATED BY TLR4 SIGNALING REPERTOIRE 1.34e-02 1.00e+00 TRIF MEDIATED TLR3 SIGNALING 1.41e-02 1.00e+00 SIGNALING BY ERBB4 1.41e-02 1.00e+00 MYD88 MAL CASCADE INITIATED ON PLASMA MEMBRANE 1.65e-02 1.00e+00 RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.45e-06 1.15e-02 psoriasis 4.06e-04 5.36e-01 decreased interleukin-9 secretion 7.73e-04 7.75e-01 abnormal CNS glial cell morphology 1.11e-03 9.56e-01 impaired neutrophil recruitment 1.22e-03 1.00e+00 increased stomach tumor incidence 1.40e-03 1.00e+00 abnormal passive avoidance behavior 2.27e-03 1.00e+00 decreased susceptibility to experimental autoimmune encephalomyelitis 3.78e-03 1.00e+00 decreased inflammatory response 4.68e-03 1.00e+00 increased interleukin-17 secretion 4.98e-03 1.00e+00 decreased interleukin-17 secretion 6.74e-03 1.00e+00 increased carcinoma incidence 7.14e-03 1.00e+00 abnormal intestinal goblet cell morphology 7.32e-03 1.00e+00 abnormal leukocyte tethering or rolling 7.49e-03 1.00e+00 abnormal nucleus accumbens morphology 7.49e-03 1.00e+00 podocyte hypertrophy 7.49e-03 1.00e+00 absent glomerular endothelium fenestra 7.49e-03 1.00e+00 podocyte microvillus transformation 7.49e-03 1.00e+00 absent podocytes 7.49e-03 1.00e+00 abnormal glomerular filtration barrier function 7.49e-03 1.00e+00 abnormal renal glomerulus basement membrane thickness

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

²FDR corrected p-value (Benjamini-Hochberg)