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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod251

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod251 Module size 17 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10668 CGRRF1 cell growth regulator with ring finger domain 1 5189 PEX1 peroxisomal biogenesis factor 1 5192 PEX10 peroxisomal biogenesis factor 10 8799 PEX11B peroxisomal biogenesis factor 11 beta 92960 PEX11G peroxisomal biogenesis factor 11 gamma 5193 PEX12 peroxisomal biogenesis factor 12 5194 PEX13 peroxisomal biogenesis factor 13 5195 PEX14 peroxisomal biogenesis factor 14 9409 PEX16 peroxisomal biogenesis factor 16 5824 PEX19 peroxisomal biogenesis factor 19 55670 PEX26 peroxisomal biogenesis factor 26 8504 PEX3 peroxisomal biogenesis factor 3 5830 PEX5 peroxisomal biogenesis factor 5 51555 PEX5L peroxisomal biogenesis factor 5 like 5190 PEX6 peroxisomal biogenesis factor 6 11264 PXMP4 peroxisomal membrane protein 4 53346 TM6SF1 transmembrane 6 superfamily member 1

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 3.70e-01 8.14e-07 GO peroxisome matrix targeting signal-1 binding molecular_function 3.63e-01 3.09e-24 GO protein import into peroxisome matrix biological_process 1.53e-01 8.80e-22 GO integral component of peroxisomal membrane cellular_component 9.97e-02 1.55e-24 GO peroxisome organization biological_process 3.25e-02 5.55e-08 GO peroxisome fission biological_process 3.11e-02 4.14e-34 GO peroxisomal membrane cellular_component

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 establishment of protein localization to organelle 0.00e+00 0.00e+00 protein transmembrane transport 0.00e+00 0.00e+00 protein targeting 0.00e+00 0.00e+00 protein import into peroxisome matrix 0.00e+00 0.00e+00 protein targeting to peroxisome 0.00e+00 0.00e+00 establishment of protein localization to peroxisome 0.00e+00 0.00e+00 intracellular protein transmembrane transport 0.00e+00 0.00e+00 peroxisome organization 0.00e+00 0.00e+00 protein localization to organelle 0.00e+00 0.00e+00 protein import 0.00e+00 0.00e+00 peroxisomal membrane transport 0.00e+00 0.00e+00 protein import into peroxisome membrane 0.00e+00 0.00e+00 peroxisomal membrane 0.00e+00 0.00e+00 peroxisome 0.00e+00 0.00e+00 integral component of peroxisomal membrane 0.00e+00 0.00e+00 intrinsic component of peroxisomal membrane 0.00e+00 0.00e+00 integral component of organelle membrane 1.76e-10 1.43e-07 protein to membrane docking 1.42e-08 9.07e-06 protein import into peroxisome matrix, docking 2.08e-08 9.02e-06 peroxisome targeting sequence binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.14e-04 1.43e-02 ABCA TRANSPORTERS IN LIPID HOMEOSTASIS 1.39e-04 1.72e-02 ABC FAMILY PROTEINS MEDIATED TRANSPORT 1.63e-04 2.40e-02 ABCA TRANSPORTERS IN LIPID HOMEOSTASIS 1.68e-04 2.46e-02 ABC FAMILY PROTEINS MEDIATED TRANSPORT 1.40e-02 1.00e+00 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.03e-04 3.52e-01 abnormal cerebral cortex morphology 2.16e-04 3.65e-01 respiratory distress 3.72e-04 5.11e-01 abnormal bile salt homeostasis 6.52e-04 7.08e-01 increased fatty acid level 2.60e-03 1.00e+00 oxidative stress 3.74e-03 1.00e+00 cholestasis 3.74e-03 1.00e+00 bile duct proliferation 3.74e-03 1.00e+00 increased saturated fatty acid level 3.74e-03 1.00e+00 increased corneal stroma thickness 3.75e-03 1.00e+00 abnormal podocyte foot process morphology 5.61e-03 1.00e+00 delayed hepatic development 6.65e-03 1.00e+00 abnormal cell morphology 7.47e-03 1.00e+00 delayed intestine development 7.47e-03 1.00e+00 abnormal corneal endothelium morphology 9.33e-03 1.00e+00 decreased Schwann cell number 9.33e-03 1.00e+00 abnormal adrenocortical cell morphology 9.33e-03 1.00e+00 abnormal circulating phospholipid level 9.33e-03 1.00e+00 iris synechia 9.89e-03 1.00e+00 hepatic steatosis 1.12e-02 1.00e+00 abnormal endplate potential

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

²FDR corrected p-value (Benjamini-Hochberg)