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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod340

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod340 Module size 29 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 25 ABL1 ABL proto-oncogene 1, non-receptor tyrosine kinase 640 BLK BLK proto-oncogene, Src family tyrosine kinase 57827 C6orf47 chromosome 6 open reading frame 47 1436 CSF1R colony stimulating factor 1 receptor 1969 EPHA2 EPH receptor A2 84553 FAXC failed axon connections homolog 2268 FGR FGR proto-oncogene, Src family tyrosine kinase 2323 FLT3LG fms related tyrosine kinase 3 ligand 2534 FYN FYN proto-oncogene, Src family tyrosine kinase 10750 GRAP GRB2 related adaptor protein 400581 GRAPL GRB2 related adaptor protein like 2888 GRB14 growth factor receptor bound protein 14 3055 HCK HCK proto-oncogene, Src family tyrosine kinase 3480 IGF1R insulin like growth factor 1 receptor 54756 IL17RD interleukin 17 receptor D 3643 INSR insulin receptor 3815 KIT KIT proto-oncogene receptor tyrosine kinase 342574 KRT27 keratin 27 79811 MET SAFB like transcription modulator 5159 PDGFRB platelet derived growth factor receptor beta 5979 RET ret proto-oncogene 56904 SH3GLB2 SH3 domain containing GRB2 like, endophilin B2 6714 SRC SRC proto-oncogene, non-receptor tyrosine kinase 8409 STAP1 ubiquitously expressed prefoldin like chaperone 8013 TEC nuclear receptor subfamily 4 group A member 3 7010 TEK TEK receptor tyrosine kinase 55321 TMEM74B transmembrane protein 74B 196740 VSTM4 V-set and transmembrane domain containing 4 7525 YES1 YES proto-oncogene 1, Src family tyrosine kinase

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 1.49e-01 1.70e-22 GO peptidyl-tyrosine autophosphorylation biological_process 1.02e-01 1.03e-05 Reactome MET activates PTK2 signaling Signal Transduction 6.21e-02 2.50e-07 GO dendritic spine maintenance biological_process 6.20e-02 7.38e-09 GO positive regulation of actin cytoskeleton reorganization biological_process 5.87e-02 2.50e-07 GO regulation of vascular permeability biological_process 5.20e-02 1.40e-17 GO transmembrane receptor protein tyrosine kinase activity molecular_function 3.03e-02 1.17e-08 GO cellular response to platelet-derived growth factor stimulus biological_process 2.38e-02 4.40e-09 Reactome Regulation of KIT signaling Signal Transduction 1.24e-02 1.67e-11 Reactome Signaling by SCF-KIT Signal Transduction 1.02e-02 1.76e-08 GO phosphatidylinositol 3-kinase binding molecular_function 8.58e-03 3.77e-10 GO positive regulation of phosphatidylinositol 3-kinase activity biological_process 7.50e-03 1.08e-16 GO transmembrane receptor protein tyrosine kinase signaling pathway biological_process

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 transmembrane receptor protein tyrosine kinase signaling pathway 0.00e+00 0.00e+00 enzyme linked receptor protein signaling pathway 0.00e+00 0.00e+00 peptidyl-tyrosine phosphorylation 0.00e+00 0.00e+00 protein autophosphorylation 0.00e+00 0.00e+00 peptidyl-tyrosine autophosphorylation 0.00e+00 0.00e+00 protein tyrosine kinase activity 0.00e+00 0.00e+00 transmembrane receptor protein tyrosine kinase activity 0.00e+00 0.00e+00 protein kinase activity 0.00e+00 0.00e+00 phosphotransferase activity, alcohol group as acceptor 0.00e+00 0.00e+00 non-membrane spanning protein tyrosine kinase activity 1.02e-10 5.25e-08 extrinsic component of cytoplasmic side of plasma membrane 1.37e-10 6.94e-08 cytoplasmic side of plasma membrane 4.13e-10 1.95e-07 cytoplasmic side of membrane 2.79e-09 1.19e-06 extrinsic component of plasma membrane 1.17e-07 3.95e-05 extrinsic component of membrane 2.94e-06 1.27e-03 regulation of actin cytoskeleton reorganization 7.30e-06 2.91e-03 Fc-gamma receptor signaling pathway involved in phagocytosis 9.48e-06 3.68e-03 Fc-gamma receptor signaling pathway 1.11e-05 4.26e-03 Fc receptor mediated stimulatory signaling pathway 1.18e-05 3.04e-03 phosphatidylinositol 3-kinase binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 6.95e-07 1.24e-04 SIGNALING BY SCF KIT 7.54e-07 1.34e-04 REGULATION OF KIT SIGNALING 7.37e-06 1.13e-03 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 8.53e-06 1.29e-03 PECAM1 INTERACTIONS 1.37e-05 2.55e-03 REGULATION OF KIT SIGNALING 1.65e-05 2.39e-03 IL 3 5 AND GM CSF SIGNALING 7.13e-05 9.33e-03 REGULATION OF SIGNALING BY CBL 1.01e-04 1.29e-02 CTLA4 INHIBITORY SIGNALING 1.16e-04 1.77e-02 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 1.29e-04 1.95e-02 SIGNALING BY SCF KIT 1.76e-04 2.57e-02 PECAM1 INTERACTIONS 3.41e-04 3.84e-02 CD28 CO STIMULATION 5.47e-04 5.88e-02 SIGNALING BY ILS 9.84e-04 9.94e-02 DCC MEDIATED ATTRACTIVE SIGNALING 1.33e-03 1.50e-01 IL 3 5 AND GM CSF SIGNALING 1.33e-03 1.50e-01 CTLA4 INHIBITORY SIGNALING 1.41e-03 1.58e-01 REGULATION OF SIGNALING BY CBL 2.18e-03 2.01e-01 COSTIMULATION BY THE CD28 FAMILY 3.76e-03 3.23e-01 TIE2 SIGNALING 3.92e-03 3.33e-01 AXON GUIDANCE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 8.53e-04 8.23e-01 distended ileum 2.57e-03 1.00e+00 abnormal motor neuron innervation pattern 3.89e-03 1.00e+00 increased interleukin-5 secretion 4.28e-03 1.00e+00 abnormal pericyte morphology 4.94e-03 1.00e+00 increased heart ventricle size 5.68e-03 1.00e+00 abnormal angiogenesis 1.08e-02 1.00e+00 disorganized myocardium 1.12e-02 1.00e+00 thin epidermis stratum spinosum 1.20e-02 1.00e+00 abnormal Sertoli cell morphology 1.22e-02 1.00e+00 decreased bone marrow cell number 1.25e-02 1.00e+00 failure of tooth eruption 1.36e-02 1.00e+00 abnormal myogenesis 1.47e-02 1.00e+00 dilated heart atrium 1.49e-02 1.00e+00 abnormal immature B cell morphology 1.51e-02 1.00e+00 abnormal vascular endothelial cell morphology 1.68e-02 1.00e+00 absent superior cervical ganglion 1.68e-02 1.00e+00 abnormal parasympathetic postganglionic fiber morphology 1.68e-02 1.00e+00 abnormal somatic motor system morphology 1.83e-02 1.00e+00 abnormal cochlear outer hair cell morphology 1.86e-02 1.00e+00 enhanced passive avoidance behavior

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

²FDR corrected p-value (Benjamini-Hochberg)