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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod126

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod126 Module size 54 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 419 ART3 ADP-ribosyltransferase 3 440087 C12orf69 single-pass membrane protein with coiled-coil domains 3 83605 CCM2 CCM2 scaffold protein 11266 DUSP1 dual specificity phosphatase 12 131096 ELK1 potassium voltage-gated channel subfamily H member 8 2004 ELK3 ELK3, ETS transcription factor 2005 ELK4 ELK4, ETS transcription factor 2115 ETV1 ETS variant 1 2116 ETV2 ETS variant 2 440695 ETV3L ETS variant 3 like 2119 ETV5 ETS variant 5 54738 FEV FEV, ETS transcription factor 2313 FLI1 Fli-1 proto-oncogene, ETS transcription factor 9653 HS2ST1 heparan sulfate 2-O-sulfotransferase 1 9884 LRRC37A leucine rich repeat containing 37A 474170 LRRC37A2 leucine rich repeat containing 37 member A2 374819 LRRC37A3 leucine rich repeat containing 37 member A3 114659 LRRC37B leucine rich repeat containing 37B 4046 LSP1 lymphocyte specific protein 1 5604 MAP2K1 mitogen-activated protein kinase kinase 1 5605 MAP2K2 mitogen-activated protein kinase kinase 2 5606 MAP2K3 mitogen-activated protein kinase kinase 3 6416 MAP2K4 mitogen-activated protein kinase kinase 4 5607 MAP2K5 mitogen-activated protein kinase kinase 5 5608 MAP2K6 mitogen-activated protein kinase kinase 6 5609 MAP2K7 mitogen-activated protein kinase kinase 7 4214 MAP3K1 mitogen-activated protein kinase kinase kinase 1 7786 MAP3K12 mitogen-activated protein kinase kinase kinase 12 4216 MAP3K4 mitogen-activated protein kinase kinase kinase 4 6885 MAP3K7 mitogen-activated protein kinase kinase kinase 7 5594 MAPK1 mitogen-activated protein kinase 1 5602 MAPK10 mitogen-activated protein kinase 10 5600 MAPK11 mitogen-activated protein kinase 11 6300 MAPK12 mitogen-activated protein kinase 12 5603 MAPK13 mitogen-activated protein kinase 13 1432 MAPK14 mitogen-activated protein kinase 14 5595 MAPK3 mitogen-activated protein kinase 3 5599 MAPK8 mitogen-activated protein kinase 8 23542 MAPK8IP2 mitogen-activated protein kinase 8 interacting protein 2 23162 MAPK8IP3 mitogen-activated protein kinase 8 interacting protein 3 5601 MAPK9 mitogen-activated protein kinase 9 9261 MAPKAPK2 mitogen-activated protein kinase-activated protein kinase 2 7867 MAPKAPK3 mitogen-activated protein kinase-activated protein kinase 3 8550 MAPKAPK5 mitogen-activated protein kinase-activated protein kinase 5 79948 MBP phospholipid phosphatase related 3 50488 MINK1 misshapen like kinase 1 2872 MKNK2 MAP kinase interacting serine/threonine kinase 2 100129480 MKRN2-AS1 MKRN2 opposite strand 5170 PDPK1 3-phosphoinositide dependent protein kinase 1 51365 PLA1A phospholipase A1 member A 23094 SIPA1L3 signal induced proliferation associated 1 like 3 27347 STK39 serine/threonine kinase 39 10454 TAB1 TGF-beta activated kinase 1 (MAP3K7) binding protein 1 284403 WDR62 WD repeat domain 62

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 4.62e-01 5.93e-32 GO MAP kinase kinase activity molecular_function 2.14e-01 9.29e-21 GO MAP kinase activity molecular_function 1.04e-01 5.82e-13 Reactome p38MAPK events Signal Transduction 8.65e-02 1.00e-16 Reactome Activation of the AP-1 family of transcription factors Immune System 6.27e-02 1.49e-16 Reactome activated TAK1 mediates p38 MAPK activation Immune System 6.21e-02 3.14e-13 Reactome Uptake and function of anthrax toxins Disease 5.76e-02 2.12e-04 GO MAP-kinase scaffold activity molecular_function 5.60e-02 6.27e-11 Reactome DSCAM interactions Developmental Biology 5.49e-02 1.60e-07 GO MAP kinase kinase kinase activity molecular_function 3.45e-02 8.15e-19 GO stress-activated protein kinase signaling cascade biological_process 1.92e-02 5.91e-15 GO JNK cascade biological_process 1.80e-02 2.62e-14 Reactome JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 Immune System 1.72e-02 4.29e-15 GO stress-activated MAPK cascade biological_process 1.12e-02 2.43e-31 Reactome Toll Like Receptor 10 (TLR10) Cascade Immune System 1.02e-02 2.43e-31 Reactome MyD88 cascade initiated on plasma membrane Immune System 9.66e-03 2.43e-31 Reactome Toll Like Receptor 5 (TLR5) Cascade Immune System 6.81e-03 6.62e-19 GO peptidyl-serine phosphorylation biological_process 4.85e-03 3.21e-18 GO signal transduction by protein phosphorylation biological_process 3.45e-03 4.57e-07 GO calmodulin-dependent protein kinase activity molecular_function 2.61e-03 3.47e-23 Reactome Oxidative Stress Induced Senescence Cellular responses to external stimuli 8.76e-04 1.06e-30 Reactome MAP kinase activation 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 0.00e+00 0.00e+00 JNK cascade 0.00e+00 0.00e+00 signal transduction by protein phosphorylation 0.00e+00 0.00e+00 activation of MAPK activity 0.00e+00 0.00e+00 stress-activated MAPK cascade 0.00e+00 0.00e+00 positive regulation of MAP kinase activity 0.00e+00 0.00e+00 MAPK cascade 0.00e+00 0.00e+00 stress-activated protein kinase signaling cascade 0.00e+00 0.00e+00 positive regulation of protein serine/threonine kinase activity 0.00e+00 0.00e+00 peptidyl-serine phosphorylation 0.00e+00 0.00e+00 proteolysis in other organism 0.00e+00 0.00e+00 signal transducer, downstream of receptor, with serine/threonine kinase activity 0.00e+00 0.00e+00 MAP kinase activity 0.00e+00 0.00e+00 protein kinase activity 0.00e+00 0.00e+00 signal transducer activity, downstream of receptor 0.00e+00 0.00e+00 protein serine/threonine kinase activity 0.00e+00 0.00e+00 phosphotransferase activity, alcohol group as acceptor 0.00e+00 0.00e+00 protein serine/threonine/tyrosine kinase activity 0.00e+00 0.00e+00 MAP kinase kinase activity 2.76e-18 2.63e-15 activation of protein kinase activity 2.85e-17 2.70e-14 regulation of MAP kinase activity

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 TRIF MEDIATED TLR3 SIGNALING 0.00e+00 0.00e+00 MAP KINASE ACTIVATION IN TLR CASCADE 0.00e+00 0.00e+00 ACTIVATED TLR4 SIGNALLING 0.00e+00 0.00e+00 TRAF6 MEDIATED INDUCTION OF NFKB AND MAP KINASES UPON TLR7 8 OR 9 ACTIVATION 0.00e+00 0.00e+00 NFKB AND MAP KINASES ACTIVATION MEDIATED BY TLR4 SIGNALING REPERTOIRE 0.00e+00 0.00e+00 TOLL RECEPTOR CASCADES 0.00e+00 0.00e+00 INNATE IMMUNE SYSTEM 0.00e+00 0.00e+00 MYD88 MAL CASCADE INITIATED ON PLASMA MEMBRANE 0.00e+00 0.00e+00 TRAF6 MEDIATED INDUCTION OF NFKB AND MAP KINASES UPON TLR7 8 OR 9 ACTIVATION 0.00e+00 0.00e+00 NFKB AND MAP KINASES ACTIVATION MEDIATED BY TLR4 SIGNALING REPERTOIRE 0.00e+00 0.00e+00 TOLL RECEPTOR CASCADES 0.00e+00 0.00e+00 TRIF MEDIATED TLR3 SIGNALING 0.00e+00 0.00e+00 INNATE IMMUNE SYSTEM 0.00e+00 0.00e+00 MYD88 MAL CASCADE INITIATED ON PLASMA MEMBRANE 0.00e+00 0.00e+00 MAP KINASE ACTIVATION IN TLR CASCADE 0.00e+00 0.00e+00 ACTIVATED TLR4 SIGNALLING 3.94e-11 1.12e-08 SIGNALLING TO RAS 8.44e-10 2.08e-07 ACTIVATION OF THE AP1 FAMILY OF TRANSCRIPTION FACTORS 1.11e-09 2.69e-07 SIGNALLING TO ERKS 1.57e-09 5.07e-07 SIGNALLING TO RAS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.91e-06 3.23e-02 decreased cardiomyocyte apoptosis 1.82e-04 3.30e-01 pale yolk sac 2.14e-04 3.64e-01 abnormal placenta development 2.44e-04 3.96e-01 decreased T cell apoptosis 4.09e-04 5.37e-01 abnormal anterior commissure pars anterior morphology 1.22e-03 1.00e+00 absent ectoplacental cone 1.28e-03 1.00e+00 abnormal placental labyrinth vasculature morphology 2.07e-03 1.00e+00 increased cardiomyocyte apoptosis 2.37e-03 1.00e+00 abnormal placenta labyrinth morphology 2.38e-03 1.00e+00 abnormal trophoblast layer morphology 2.93e-03 1.00e+00 abnormal anterior commissure pars posterior morphology 5.38e-03 1.00e+00 abnormal anterior commissure morphology 6.40e-03 1.00e+00 abnormal keratinocyte morphology 7.80e-03 1.00e+00 abnormal first pharyngeal arch morphology 7.84e-03 1.00e+00 poor circulation 8.19e-03 1.00e+00 decreased myocardial infarction size 8.91e-03 1.00e+00 hypotension 1.01e-02 1.00e+00 thin myocardium 1.03e-02 1.00e+00 abnormal keratinocyte differentiation 1.06e-02 1.00e+00 abnormal angiogenesis

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

²FDR corrected p-value (Benjamini-Hochberg)