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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod131

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod131 Module size 22 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 23204 ARL6IP1 ADP ribosylation factor like GTPase 6 interacting protein 1 127687 C1orf122 chromosome 1 open reading frame 122 64855 FAM129B family with sequence similarity 129 member B 80148 PQLC1 PQ loop repeat containing 1 6642 SNX1 sorting nexin 1 29887 SNX10 sorting nexin 10 29916 SNX11 sorting nexin 11 29934 SNX12 sorting nexin 12 6643 SNX2 sorting nexin 2 8724 SNX3 sorting nexin 3 401548 SNX30 sorting nexin family member 30 254122 SNX32 sorting nexin 32 27131 SNX5 sorting nexin 5 58533 SNX6 sorting nexin 6 51375 SNX7 sorting nexin 7 29886 SNX8 sorting nexin 8 6653 SORL1 sortilin related receptor 1 9559 VPS26A VPS26, retromer complex component A 112936 VPS26B VPS26, retromer complex component B 51699 VPS29 VPS29, retromer complex component 55737 VPS35 VPS35, retromer complex component 92715 WDR85 diphthamide biosynthesis 7

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 3.02e-01 4.58e-26 GO retromer complex cellular_component 1.42e-02 2.75e-07 GO early endosome to Golgi transport biological_process 5.84e-03 1.05e-08 Reactome WNT ligand biogenesis and trafficking Signal Transduction 3.83e-03 3.77e-11 GO regulation of macroautophagy 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 cytosolic transport 0.00e+00 0.00e+00 endosomal transport 0.00e+00 0.00e+00 retrograde transport, endosome to Golgi 0.00e+00 0.00e+00 vesicle organization 0.00e+00 0.00e+00 endocytosis 0.00e+00 0.00e+00 early endosome 0.00e+00 0.00e+00 endosome 0.00e+00 0.00e+00 retromer complex 0.00e+00 0.00e+00 extrinsic component of membrane 0.00e+00 0.00e+00 phosphatidylinositol binding 0.00e+00 0.00e+00 lipid binding 0.00e+00 0.00e+00 phospholipid binding 1.15e-10 5.87e-08 retromer, cargo-selective complex 2.66e-10 1.30e-07 tubular endosome 3.14e-10 1.51e-07 retromer, tubulation complex 9.80e-10 4.39e-07 endosome membrane 5.99e-09 4.01e-06 regulation of macroautophagy 1.29e-08 8.29e-06 regulation of autophagy 1.66e-07 9.03e-05 early endosome to Golgi transport 4.43e-07 1.37e-04 early endosome membrane

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.74e-04 3.78e-02 GOLGI ASSOCIATED VESICLE BIOGENESIS 3.44e-04 4.63e-02 TRANS GOLGI NETWORK VESICLE BUDDING 4.52e-04 4.95e-02 GOLGI ASSOCIATED VESICLE BIOGENESIS 6.00e-04 6.38e-02 TRANS GOLGI NETWORK VESICLE BUDDING 1.42e-03 1.37e-01 MEMBRANE TRAFFICKING 1.54e-03 1.71e-01 MEMBRANE TRAFFICKING

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 decreased bone trabecular spacing 1.87e-03 1e+00 decreased vitamin D level 1.87e-03 1e+00 increased osteoid volume 1.87e-03 1e+00 decreased bone stiffness 3.74e-03 1e+00 loss of dopaminergic neurons 3.74e-03 1e+00 alpha-synuclein inclusion body 3.74e-03 1e+00 tau protein deposits 3.74e-03 1e+00 decreased type I pneumocyte number 5.61e-03 1e+00 abnormal dopaminergic neuron morphology 5.61e-03 1e+00 failure of tooth eruption 5.61e-03 1e+00 abnormal cholinergic neuron morphology 7.47e-03 1e+00 increased stomach pH 7.47e-03 1e+00 rickets 7.47e-03 1e+00 osteomalacia 7.47e-03 1e+00 amyloid beta deposits 7.47e-03 1e+00 abnormal chorioallantoic fusion 7.48e-03 1e+00 decreased lung weight 1.12e-02 1e+00 osteopetrosis 1.12e-02 1e+00 abnormal gastric chief cell morphology 1.12e-02 1e+00 increased circulating parathyroid hormone level

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

²FDR corrected p-value (Benjamini-Hochberg)