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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod329

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod329 Module size 12 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 25798 BRI3 brain protein I3 752 FMNL1 formin like 1 114793 FMNL2 formin like 2 91010 FMNL3 formin like 3 51125 GOLGA7 golgin A7 401647 GOLGA7B golgin A7 family member B 9741 LAPTM4A lysosomal protein transmembrane 4 alpha 55353 LAPTM4B lysosomal protein transmembrane 4 beta 619189 SERINC4 serine incorporator 4 202915 TMEM184A transmembrane protein 184A 25829 TMEM184B transmembrane protein 184B 55751 TMEM184C transmembrane protein 184C

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 2.56e-03 2.77e-05 GO GTPase activating protein binding molecular_function

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 7.41e-06 1.98e-03 Rho GTPase binding 2.15e-05 5.26e-03 GTPase activating protein binding 2.16e-05 7.68e-03 peptidyl-L-cysteine S-palmitoylation 4.91e-05 1.58e-02 regulation of cell morphogenesis 5.58e-05 1.17e-02 palmitoyltransferase complex 9.91e-05 2.90e-02 protein palmitoylation 1.26e-04 3.56e-02 cortical actin cytoskeleton organization 1.27e-04 3.58e-02 cortical cytoskeleton organization 2.49e-04 6.30e-02 actin cytoskeleton organization 3.33e-04 8.02e-02 actin filament-based process 5.13e-04 8.59e-02 protein-cysteine S-palmitoyltransferase activity 5.22e-04 1.16e-01 protein localization to plasma membrane 5.60e-04 9.28e-02 Ras GTPase binding 7.04e-04 1.13e-01 palmitoyltransferase activity 7.28e-04 1.17e-01 small GTPase binding 8.44e-04 1.33e-01 GTPase binding 8.53e-04 1.73e-01 plasma membrane organization 9.94e-04 1.96e-01 regulation of cell shape 1.48e-03 2.17e-01 actin binding 2.25e-03 3.75e-01 protein lipidation

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

²FDR corrected p-value (Benjamini-Hochberg)