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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod34

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod34 Module size 39 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 7813 EVI5 ecotropic viral integration site 5 115704 EVI5L ecotropic viral integration site 5 like 131583 FAM43A family with sequence similarity 43 member A 79774 GRTP1 growth hormone regulated TBC protein 1 401258 RAB44 RAB44, member RAS oncogene family 23637 RABGAP1 RAB GTPase activating protein 1 9910 RABGAP1L RAB GTPase activating protein 1 like 158158 RASEF RAS and EF-hand domain containing 129049 SGSM1 small G protein signaling modulator 1 9905 SGSM2 small G protein signaling modulator 2 27352 SGSM3 small G protein signaling modulator 3 221178 SPATA13 spermatogenesis associated 13 23216 TBC1D1 TBC1 domain family member 1 23232 TBC1D12 TBC1 domain family member 12 54662 TBC1D13 TBC1 domain family member 13 57533 TBC1D14 TBC1 domain family member 14 64786 TBC1D15 TBC1 domain family member 15 125058 TBC1D16 TBC1 domain family member 16 79735 TBC1D17 TBC1 domain family member 17 55357 TBC1D2 TBC1 domain family member 2 161514 TBC1D21 TBC1 domain family member 21 4943 TBC1D25 TBC1 domain family member 25 353149 TBC1D26 TBC1 domain family member 26 254272 TBC1D28 TBC1 domain family member 28 26083 TBC1D29 TBC1 domain family member 29, pseudogene 23102 TBC1D2B TBC1 domain family member 2B 101060389 TBC1D3 TBC1 domain family member 3D 23329 TBC1D30 TBC1 domain family member 30 414059 TBC1D3B TBC1 domain family member 3B 414060 TBC1D3C TBC1 domain family member 3C 729873 TBC1D3F TBC1 domain family member 3 101060321 TBC1D3G TBC1 domain family member 3G 101060389 TBC1D3H TBC1 domain family member 3D 11138 TBC1D8 TBC1 domain family member 8 54885 TBC1D8B TBC1 domain family member 8B 23158 TBC1D9 TBC1 domain family member 9 23061 TBC1D9B TBC1 domain family member 9B 9098 USP6 ubiquitin specific peptidase 6 9712 USP6NL USP6 N-terminal like

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 2.61e-01 2.73e-77 GO activation of GTPase activity biological_process 1.46e-01 1.22e-33 GO regulation of cilium 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 vesicle fusion 0.00e+00 0.00e+00 activation of GTPase activity 0.00e+00 0.00e+00 regulation of GTPase activity 0.00e+00 0.00e+00 regulation of vesicle-mediated transport 0.00e+00 0.00e+00 positive regulation of GTPase activity 0.00e+00 0.00e+00 regulation of cell projection assembly 0.00e+00 0.00e+00 regulation of cilium assembly 0.00e+00 0.00e+00 regulation of organelle assembly 0.00e+00 0.00e+00 regulation of cell projection organization 0.00e+00 0.00e+00 GTPase binding 0.00e+00 0.00e+00 GTPase activator activity 0.00e+00 0.00e+00 small GTPase binding 0.00e+00 0.00e+00 enzyme activator activity 0.00e+00 0.00e+00 GTPase regulator activity 0.00e+00 0.00e+00 Rab GTPase binding 0.00e+00 0.00e+00 Ras GTPase binding 2.71e-06 7.35e-04 autophagosome 5.05e-06 2.09e-03 endosomal transport 5.76e-06 1.48e-03 recycling endosome 7.15e-06 2.86e-03 regulation of vacuole organization

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.82e-02 1e+00 GOLGI ASSOCIATED VESICLE BIOGENESIS 1.92e-02 1e+00 TRANS GOLGI NETWORK VESICLE BUDDING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.88e-03 1e+00 increased white adipose tissue amount 3.75e-03 1e+00 increased basal metabolism 7.47e-03 1e+00 abnormal fatty acid oxidation 7.49e-03 1e+00 decreased respiratory quotient 9.36e-03 1e+00 decreased circulating total protein level 1.49e-02 1e+00 abnormal muscle cell glucose uptake 1.93e-02 1e+00 abnormal homeostasis 2.01e-02 1e+00 decreased lean body mass 2.24e-02 1e+00 increased lean body mass 2.25e-02 1e+00 increased mean corpuscular volume 2.62e-02 1e+00 increased bone mineral density 2.69e-02 1e+00 increased circulating cholesterol level 2.73e-02 1e+00 increased startle reflex 2.91e-02 1e+00 increased rib number 2.93e-02 1e+00 increased heart weight 3.17e-02 1e+00 decreased susceptibility to diet-induced obesity 3.18e-02 1e+00 increased circulating insulin level 3.58e-02 1e+00 decreased circulating glucose level 3.60e-02 1e+00 decreased total body fat amount 4.36e-02 1e+00 complete embryonic lethality between implantation and placentation

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

²FDR corrected p-value (Benjamini-Hochberg)