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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod200

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod200 Module size 57 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 285598 ARL10 ADP ribosylation factor like GTPase 10 148252 DIRAS1 DIRAS family GTPase 1 54769 DIRAS2 DIRAS family GTPase 2 9077 DIRAS3 DIRAS family GTPase 3 3266 ERAS ES cell expressed Ras 2669 GEM GTP binding protein overexpressed in skeletal muscle 22808 MRAS muscle RAS oncogene homolog 375189 PFN4 profilin family member 4 5899 RALB RAS like proto-oncogene B 5911 RAP2A RAP2A, member of RAS oncogene family 5912 RAP2B RAP2B, member of RAS oncogene family 57826 RAP2C RAP2C, member of RAS oncogene family 64926 RASAL3 RAS protein activator like 3 51655 RASD1 ras related dexamethasone induced 1 23551 RASD2 RASD family member 2 153020 RASGEF1B RasGEF domain family member 1B 10633 RASL10A RAS like family 10 member A 91608 RASL10B RAS like family 10 member B 387496 RASL11A RAS like family 11 member A 65997 RASL11B RAS like family 11 member B 51285 RASL12 RAS like family 12 28954 REM1 RRAD and GEM like GTPase 1 161253 REM2 RRAD and GEM like GTPase 2 85004 RERG RAS like estrogen regulated growth inhibitor 79785 RERGL RERG like 57139 RGL3 ral guanine nucleotide dissociation stimulator like 3 266747 RGL4 ral guanine nucleotide dissociation stimulator like 4 6009 RHEB Ras homolog, mTORC1 binding 121268 RHEBL1 RHEB like 1 22836 RHOBTB3 Rho related BTB domain containing 3 6016 RIT1 Ras like without CAAX 1 6014 RIT2 Ras like without CAAX 2 27289 RND1 Rho family GTPase 1 8153 RND2 Rho family GTPase 2 390 RND3 Rho family GTPase 3 6236 RRAD RRAD, Ras related glycolysis inhibitor and calcium channel regulator 22800 RRAS2 RAS related 2 79363 RSG1 ciliogenesis and planar polarity effector 2 29800 ZDHHC1 zinc finger DHHC-type containing 1 79844 ZDHHC11 zinc finger DHHC-type containing 11 653082 ZDHHC11B zinc finger DHHC-type containing 11B 84885 ZDHHC12 zinc finger DHHC-type containing 12 79683 ZDHHC14 zinc finger DHHC-type containing 14 158866 ZDHHC15 zinc finger DHHC-type containing 15 84243 ZDHHC18 zinc finger DHHC-type containing 18 131540 ZDHHC19 zinc finger DHHC-type containing 19 51201 ZDHHC2 zinc finger DHHC-type containing 2 253832 ZDHHC20 zinc finger DHHC-type containing 20 340481 ZDHHC21 zinc finger DHHC-type containing 21 283576 ZDHHC22 zinc finger DHHC-type containing 22 254887 ZDHHC23 zinc finger DHHC-type containing 23 254359 ZDHHC24 zinc finger DHHC-type containing 24 51304 ZDHHC3 zinc finger DHHC-type containing 3 25921 ZDHHC5 zinc finger DHHC-type containing 5 64429 ZDHHC6 zinc finger DHHC-type containing 6 55625 ZDHHC7 zinc finger DHHC-type containing 7 29801 ZDHHC8 zinc finger DHHC-type containing 8

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 3.17e-01 9.35e-41 GO peptidyl-L-cysteine S-palmitoylation biological_process 2.24e-01 2.81e-44 GO protein-cysteine S-palmitoyltransferase activity molecular_function 1.44e-01 8.26e-05 Reactome Signalling to p38 via RIT and RIN Signal Transduction 1.08e-01 1.14e-33 GO protein palmitoylation biological_process 8.62e-02 3.77e-06 GO Rap protein signal transduction biological_process 6.77e-02 1.66e-30 GO palmitoyltransferase activity molecular_function 5.64e-02 1.06e-15 GO small GTPase mediated signal transduction biological_process 4.99e-02 6.50e-06 GO establishment or maintenance of actin cytoskeleton polarity biological_process 3.39e-02 3.93e-10 GO GDP binding molecular_function 5.92e-03 1.53e-05 GO microvillus assembly biological_process 3.71e-03 3.95e-05 GO positive regulation of protein autophosphorylation 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 small GTPase mediated signal transduction 0.00e+00 0.00e+00 protein lipidation 0.00e+00 0.00e+00 protein palmitoylation 0.00e+00 0.00e+00 lipoprotein metabolic process 0.00e+00 0.00e+00 lipoprotein biosynthetic process 0.00e+00 0.00e+00 purine nucleoside binding 0.00e+00 0.00e+00 GTP binding 0.00e+00 0.00e+00 ribonucleoside binding 0.00e+00 0.00e+00 guanyl ribonucleotide binding 0.00e+00 0.00e+00 nucleoside binding 0.00e+00 0.00e+00 protein-cysteine S-palmitoyltransferase activity 0.00e+00 0.00e+00 palmitoyltransferase activity 3.93e-18 2.80e-15 GTPase activity 3.02e-17 2.13e-14 transferase activity, transferring acyl groups 1.68e-11 1.09e-08 nucleoside-triphosphatase activity 4.89e-10 3.77e-07 Ras protein signal transduction 4.28e-07 2.18e-04 Rap protein signal transduction 1.74e-06 7.91e-04 positive regulation of protein autophosphorylation 2.42e-06 6.64e-04 recycling endosome membrane 2.92e-06 1.27e-03 regulation of protein autophosphorylation

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 5.78e-07 1.35e-04 SIGNALLING TO ERKS 1.89e-06 3.15e-04 SIGNALLING TO ERKS 4.12e-06 8.36e-04 NGF SIGNALLING VIA TRKA FROM THE PLASMA MEMBRANE 7.11e-06 1.09e-03 NGF SIGNALLING VIA TRKA FROM THE PLASMA MEMBRANE 2.00e-05 3.61e-03 SIGNALLING TO P38 VIA RIT AND RIN 2.65e-05 3.71e-03 SIGNALLING TO P38 VIA RIT AND RIN 1.75e-04 2.55e-02 SIGNALLING BY NGF 3.97e-04 4.41e-02 SIGNALLING BY NGF 3.44e-03 3.35e-01 REGULATION OF RHEB GTPASE ACTIVITY BY AMPK 6.86e-03 5.92e-01 MTORC1 MEDIATED SIGNALLING 6.86e-03 5.92e-01 P38MAPK EVENTS 6.87e-03 5.92e-01 SIGNALLING TO RAS 1.26e-02 8.86e-01 MTORC1 MEDIATED SIGNALLING 1.26e-02 8.86e-01 P38MAPK EVENTS 1.32e-02 9.91e-01 ENOS ACTIVATION AND REGULATION 1.54e-02 1.00e+00 ENERGY DEPENDENT REGULATION OF MTOR BY LKB1 AMPK 1.71e-02 1.00e+00 SEMA3A PLEXIN REPULSION SIGNALING BY INHIBITING INTEGRIN ADHESION 1.79e-02 1.00e+00 REGULATION OF RHEB GTPASE ACTIVITY BY AMPK 1.80e-02 1.00e+00 SIGNALLING TO RAS 1.88e-02 1.00e+00 PKB MEDIATED EVENTS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.87e-03 1e+00 abnormal hair shaft melanin granule morphology 1.87e-03 1e+00 cerebral aqueductal stenosis 3.74e-03 1e+00 sebaceous gland hyperplasia 3.74e-03 1e+00 epidermal cyst 3.74e-03 1e+00 positive geotaxis 3.75e-03 1e+00 abnormal ear development 4.72e-03 1e+00 increased total body fat amount 5.61e-03 1e+00 abnormal brain ventricular system morphology 5.61e-03 1e+00 abnormal brain ependyma morphology 7.18e-03 1e+00 abnormal motor capabilities/coordination/movement 7.47e-03 1e+00 abnormal sebaceous gland physiology 7.48e-03 1e+00 matted coat 7.48e-03 1e+00 premature hair loss 7.48e-03 1e+00 abnormal tibialis anterior morphology 9.34e-03 1e+00 abnormal hypaxial muscle morphology 1.12e-02 1e+00 short hair 1.12e-02 1e+00 abnormal dendritic cell morphology 1.12e-02 1e+00 abnormal patella morphology 1.31e-02 1e+00 greasy coat 1.31e-02 1e+00 abnormal cerebral aqueduct morphology

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

²FDR corrected p-value (Benjamini-Hochberg)