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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod83

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod83 Module size 23 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 79058 ASPSCR1 ASPSCR1, UBX domain containing tether for SLC2A4 23265 EXOC1 exocyst complex component 7 55770 EXOC2 exocyst complex component 2 11336 EXOC3 exocyst complex component 3 283849 EXOC3L1 exocyst complex component 3 like 1 90332 EXOC3L2 exocyst complex component 3 like 2 91828 EXOC3L4 exocyst complex component 3 like 4 60412 EXOC4 exocyst complex component 4 10640 EXOC5 exocyst complex component 5 54536 EXOC6 exocyst complex component 6 23233 EXOC6B exocyst complex component 6B 23265 EXOC7 exocyst complex component 7 149371 EXOC8 exocyst complex component 8 4622 MYH4 myosin heavy chain 4 10890 RAB10 RAB10, member RAS oncogene family 5872 RAB13 RAB13, member RAS oncogene family 51552 RAB14 RAB14, member RAS oncogene family 5866 RAB3IL1 RAB3A interacting protein like 1 117177 RAB3IP RAB3A interacting protein 4218 RAB8A RAB8A, member RAS oncogene family 5898 RALA RAS like proto-oncogene A 6814 STXBP3 syntaxin binding protein 3 7127 TNFAIP2 TNF alpha induced protein 2

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 4.58e-01 4.27e-39 GO exocyst cellular_component 1.23e-01 6.52e-25 Reactome VxPx cargo-targeting to cilium Organelle biogenesis and maintenance 1.18e-01 1.43e-34 Reactome Translocation of SLC2A4 (GLUT4) to the plasma membrane Vesicle-mediated transport 5.57e-03 3.07e-12 GO vesicle docking involved in exocytosis 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 membrane docking 0.00e+00 0.00e+00 exocytosis 0.00e+00 0.00e+00 vesicle docking 0.00e+00 0.00e+00 vesicle docking involved in exocytosis 0.00e+00 0.00e+00 cellular protein complex localization 0.00e+00 0.00e+00 exocyst localization 0.00e+00 0.00e+00 exocyst 0.00e+00 0.00e+00 cell cortex 9.37e-11 7.80e-08 protein complex localization 2.71e-09 1.91e-06 Golgi to plasma membrane transport 2.85e-09 2.00e-06 post-Golgi vesicle-mediated transport 7.54e-09 3.49e-06 Ral GTPase binding 2.05e-08 8.90e-06 SNARE binding 3.78e-07 1.94e-04 Golgi vesicle transport 2.29e-06 6.80e-04 GDP binding 3.83e-06 1.09e-03 myosin binding 6.50e-06 1.76e-03 Ras GTPase binding 9.25e-06 2.43e-03 small GTPase binding 1.29e-05 3.29e-03 myosin V binding 1.39e-05 3.52e-03 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 INSULIN SYNTHESIS AND PROCESSING 0.00e+00 0.00e+00 INSULIN SYNTHESIS AND PROCESSING 2.04e-10 5.39e-08 DIABETES PATHWAYS 2.26e-10 7.96e-08 DIABETES PATHWAYS 1.72e-03 1.87e-01 P38MAPK EVENTS 3.44e-03 3.35e-01 SIGNALLING TO RAS 5.43e-03 4.39e-01 P38MAPK EVENTS 5.44e-03 4.40e-01 SIGNALLING TO RAS 7.26e-03 5.63e-01 SIGNALLING TO ERKS 1.37e-02 1.00e+00 SIGNALLING TO ERKS 2.60e-02 1.00e+00 NGF SIGNALLING VIA TRKA FROM THE PLASMA MEMBRANE 3.18e-02 1.00e+00 NGF SIGNALLING VIA TRKA FROM THE PLASMA MEMBRANE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.74e-03 1e+00 hyperchromasia 3.75e-03 1e+00 decreased skeletal muscle fiber number 5.61e-03 1e+00 hypochromic anemia 5.61e-03 1e+00 increased erythrocyte protoporphyrin level 5.61e-03 1e+00 microcytic anemia 5.61e-03 1e+00 delayed gastrulation 5.61e-03 1e+00 accumulation of giant lysosomes in kidney/renal tubule cells 7.47e-03 1e+00 embryonic lethality prior to tooth bud stage 7.47e-03 1e+00 absent amniotic cavity 7.48e-03 1e+00 myositis 9.35e-03 1e+00 poikilocytosis 1.12e-02 1e+00 skeletal muscle fiber degeneration 1.12e-02 1e+00 decreased paraxial mesoderm size 1.12e-02 1e+00 abnormal intestinal absorption 1.30e-02 1e+00 macrocytosis 1.31e-02 1e+00 abnormal snout morphology 1.31e-02 1e+00 microcytosis 1.31e-02 1e+00 polychromatophilia 1.33e-02 1e+00 partial preweaning lethality 1.49e-02 1e+00 abnormal proerythroblast morphology

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

²FDR corrected p-value (Benjamini-Hochberg)