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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod46

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod46 Module size 59 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 29 ABR ABR, RhoGEF and GTPase activating protein 11214 AKAP13 A-kinase anchoring protein 13 116985 ARAP1 ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 64411 ARAP3 ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3 79658 ARHGAP10 Rho GTPase activating protein 10 94134 ARHGAP12 Rho GTPase activating protein 12 55843 ARHGAP15 Rho GTPase activating protein 15 93663 ARHGAP18 Rho GTPase activating protein 18 84986 ARHGAP19 Rho GTPase activating protein 19 57569 ARHGAP20 Rho GTPase activating protein 20 58504 ARHGAP22 Rho GTPase activating protein 22 57636 ARHGAP23 Rho GTPase activating protein 23 83478 ARHGAP24 Rho GTPase activating protein 24 9938 ARHGAP25 Rho GTPase activating protein 25 79822 ARHGAP28 Rho GTPase activating protein 28 9411 ARHGAP29 Rho GTPase activating protein 29 257106 ARHGAP30 Rho GTPase activating protein 30 57514 ARHGAP31 Rho GTPase activating protein 31 115703 ARHGAP33 Rho GTPase activating protein 33 158763 ARHGAP36 Rho GTPase activating protein 36 80728 ARHGAP39 Rho GTPase activating protein 39 343578 ARHGAP40 Rho GTPase activating protein 40 9912 ARHGAP44 Rho GTPase activating protein 44 23779 ARHGAP8 Rho GTPase activating protein 8 64333 ARHGAP9 Rho GTPase activating protein 9 396 ARHGDIA Rho GDP dissociation inhibitor alpha 397 ARHGDIB Rho GDP dissociation inhibitor beta 398 ARHGDIG Rho GDP dissociation inhibitor gamma 27237 ARHGEF16 Rho guanine nucleotide exchange factor 16 9828 ARHGEF17 Rho guanine nucleotide exchange factor 17 23370 ARHGEF18 Rho/Rac guanine nucleotide exchange factor 18 9181 ARHGEF2 Rho/Rac guanine nucleotide exchange factor 2 50649 ARHGEF4 Rho guanine nucleotide exchange factor 4 55789 DEPDC1B DEP domain containing 1B 91614 DEPDC7 DEP domain containing 7 10144 FAM13A family with sequence similarity 13 member A 51306 FAM13B family with sequence similarity 13 member B 2245 FGD1 FYVE, RhoGEF and PH domain containing 1 56246 FGD2 melanocortin 2 receptor accessory protein 89846 FGD3 FYVE, RhoGEF and PH domain containing 3 121512 FGD4 FYVE, RhoGEF and PH domain containing 4 51291 GMIP GEM interacting protein 23526 HMHA1 Rho GTPase activating protein 45 8997 KALRN kalirin RhoGEF kinase 4168 MCF2 MCF.2 cell line derived transforming sequence 23263 MCF2L MCF.2 cell line derived transforming sequence like 4983 OPHN1 oligophrenin 1 64857 PLEKHG2 pleckstrin homology and RhoGEF domain containing G2 57449 PLEKHG5 pleckstrin homology and RhoGEF domain containing G5 89941 RHOT2 ras homolog family member T2 57522 SRGAP1 SLIT-ROBO Rho GTPase activating protein 1 9901 SRGAP3 SLIT-ROBO Rho GTPase activating protein 3 90627 STARD13 StAR related lipid transfer domain containing 13 9754 STARD8 StAR related lipid transfer domain containing 8 85360 SYDE1 synapse defective Rho GTPase homolog 1 84144 SYDE2 synapse defective Rho GTPase homolog 2 117289 TAGAP T cell activation RhoGTPase activating protein 26230 TIAM2 T cell lymphoma invasion and metastasis 2 9322 TRIP10 thyroid hormone receptor interactor 10

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 2.15e-01 6.08e-130 Reactome Rho GTPase cycle Signal Transduction 1.70e-01 7.37e-126 GO regulation of small GTPase mediated signal transduction biological_process 8.44e-03 3.33e-09 GO filopodium assembly 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 regulation of small GTPase mediated signal transduction 0.00e+00 0.00e+00 regulation of GTPase activity 0.00e+00 0.00e+00 positive regulation of GTPase activity 0.00e+00 0.00e+00 regulation of Rho protein signal transduction 0.00e+00 0.00e+00 regulation of Ras protein signal transduction 0.00e+00 0.00e+00 GTPase activator activity 0.00e+00 0.00e+00 enzyme activator activity 0.00e+00 0.00e+00 GTPase regulator activity 2.49e-20 1.80e-17 Rho guanyl-nucleotide exchange factor activity 4.51e-15 4.24e-12 positive regulation of apoptotic process 4.90e-15 4.61e-12 positive regulation of programmed cell death 1.29e-14 1.21e-11 positive regulation of cell death 3.77e-13 2.62e-10 Ras guanyl-nucleotide exchange factor activity 1.07e-12 7.40e-10 guanyl-nucleotide exchange factor activity 7.58e-11 3.97e-08 cell leading edge 4.65e-10 3.60e-07 regulation of cell shape 4.97e-10 3.83e-07 regulation of cell morphogenesis 2.22e-09 9.57e-07 lamellipodium 3.34e-09 2.32e-06 filopodium assembly 1.60e-08 7.08e-06 small GTPase binding

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 SIGNALING BY RHO GTPASES 0.00e+00 0.00e+00 P75 NTR RECEPTOR MEDIATED SIGNALLING 0.00e+00 0.00e+00 NRAGE SIGNALS DEATH THROUGH JNK 0.00e+00 0.00e+00 SIGNALLING BY NGF 0.00e+00 0.00e+00 G ALPHA1213 SIGNALLING EVENTS 0.00e+00 0.00e+00 CELL DEATH SIGNALLING VIA NRAGE NRIF AND NADE 0.00e+00 0.00e+00 SIGNALING BY RHO GTPASES 0.00e+00 0.00e+00 P75 NTR RECEPTOR MEDIATED SIGNALLING 0.00e+00 0.00e+00 NRAGE SIGNALS DEATH THROUGH JNK 0.00e+00 0.00e+00 SIGNALLING BY NGF 0.00e+00 0.00e+00 G ALPHA1213 SIGNALLING EVENTS 0.00e+00 0.00e+00 CELL DEATH SIGNALLING VIA NRAGE NRIF AND NADE 1.04e-03 1.04e-01 SIGNALING BY ROBO RECEPTOR 5.42e-03 4.88e-01 SIGNALING BY ROBO RECEPTOR 4.14e-02 1.00e+00 TGF BETA RECEPTOR SIGNALING IN EMT EPITHELIAL TO MESENCHYMAL TRANSITION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.26e-05 5.58e-02 abnormal dendrite morphology 9.57e-04 8.82e-01 abnormal tumor vascularization 3.02e-03 1.00e+00 abnormal sarcomere morphology 3.75e-03 1.00e+00 mesangial cell hypoplasia 3.75e-03 1.00e+00 absent podocytes 6.14e-03 1.00e+00 thin cerebral cortex 6.87e-03 1.00e+00 decreased B cell number 7.48e-03 1.00e+00 cerebral edema 7.72e-03 1.00e+00 abnormal spatial working memory 8.87e-03 1.00e+00 abnormal angiogenesis 9.34e-03 1.00e+00 abnormal renal/urinary system physiology 9.35e-03 1.00e+00 abnormal glomerular mesangium morphology 1.02e-02 1.00e+00 decreased angiogenesis 1.10e-02 1.00e+00 abnormal action potential 1.12e-02 1.00e+00 abnormal miniature excitatory postsynaptic currents 1.12e-02 1.00e+00 reduced AMPA-mediated synaptic currents 1.30e-02 1.00e+00 abnormal aggression-related behavior 1.30e-02 1.00e+00 increased transitional stage T1 B cell number 1.30e-02 1.00e+00 abnormal parietal lobe morphology 1.31e-02 1.00e+00 abnormal distal convoluted tubule morphology

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

²FDR corrected p-value (Benjamini-Hochberg)