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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod93

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod93 Module size 18 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 100128327 BET3L trafficking protein particle complex 3 like 80006 C5orf44 trafficking protein particle complex 13 83445 GSG1 germ cell associated 1 112611 RWDD2A RWD domain containing 2A 58485 TRAPPC1 trafficking protein particle complex 1 309678 TRAPPC10 trafficking protein particle complex 10 60684 TRAPPC11 trafficking protein particle complex 11 51112 TRAPPC12 trafficking protein particle complex 12 6399 TRAPPC2 trafficking protein particle complex 2 51693 TRAPPC2L trafficking protein particle complex 2 like 10597 TRAPPC2P1 trafficking protein particle complex 2B 27095 TRAPPC3 trafficking protein particle complex 3 51399 TRAPPC4 trafficking protein particle complex 4 126003 TRAPPC5 trafficking protein particle complex 5 79090 TRAPPC6A trafficking protein particle complex 6A 122553 TRAPPC6B trafficking protein particle complex 6B 22878 TRAPPC8 trafficking protein particle complex 8 83696 TRAPPC9 trafficking protein particle complex 9

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 6.47e-01 4.56e-36 GO TRAPP complex cellular_component 2.49e-02 3.68e-33 GO Rab guanyl-nucleotide exchange factor activity molecular_function 5.96e-03 2.06e-22 GO COPII vesicle coating 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 COPII-coated vesicle budding 0.00e+00 0.00e+00 positive regulation of GTPase activity 0.00e+00 0.00e+00 COPII vesicle coating 0.00e+00 0.00e+00 vesicle targeting, to, from or within Golgi 0.00e+00 0.00e+00 ER to Golgi vesicle-mediated transport 0.00e+00 0.00e+00 organelle localization 0.00e+00 0.00e+00 membrane budding 0.00e+00 0.00e+00 vesicle organization 0.00e+00 0.00e+00 establishment of vesicle localization 0.00e+00 0.00e+00 vesicle targeting 0.00e+00 0.00e+00 regulation of GTPase activity 0.00e+00 0.00e+00 vesicle localization 0.00e+00 0.00e+00 Golgi vesicle transport 0.00e+00 0.00e+00 establishment of organelle localization 0.00e+00 0.00e+00 TRAPP complex 0.00e+00 0.00e+00 Golgi membrane 0.00e+00 0.00e+00 guanyl-nucleotide exchange factor activity 0.00e+00 0.00e+00 Ras guanyl-nucleotide exchange factor activity 0.00e+00 0.00e+00 Rab guanyl-nucleotide exchange factor activity 3.66e-04 6.17e-02 trans-Golgi network

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

²FDR corrected p-value (Benjamini-Hochberg)