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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod304

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod304 Module size 32 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 92482 BBIP1 BBSome interacting protein 1 582 BBS1 Bardet-Biedl syndrome 1 166379 BBS12 Bardet-Biedl syndrome 12 583 BBS2 Bardet-Biedl syndrome 2 129880 BBS5 Bardet-Biedl syndrome 5 55212 BBS7 Bardet-Biedl syndrome 7 27241 BBS9 Bardet-Biedl syndrome 9 256646 C15orf55 NUT midline carcinoma family member 1 79140 CCDC28B coiled-coil domain containing 28B 1038 CDR1 cerebellar degeneration related protein 1 23065 EMC1 ER membrane protein complex subunit 1 284361 EMC10 ER membrane protein complex subunit 10 9694 EMC2 ER membrane protein complex subunit 2 55831 EMC3 ER membrane protein complex subunit 3 51234 EMC4 ER membrane protein complex subunit 4 83460 EMC6 ER membrane protein complex subunit 6 56851 EMC7 ER membrane protein complex subunit 7 10328 EMC8 ER membrane protein complex subunit 8 51016 EMC9 ER membrane protein complex subunit 9 29109 FHOD1 formin homology 2 domain containing 1 55890 GPRC5C G protein-coupled receptor class C group 5 member C 79663 HSPBAP1 HSPB1 associated protein 1 54585 LZTFL1 leucine zipper transcription factor like 1 93380 MMGT1 membrane magnesium transporter 1 56926 NCLN nicalin 132299 OCIAD2 OCIA domain containing 2 9552 SPAG7 sperm associated antigen 7 79853 TM4SF20 transmembrane 4 L six family member 20 54499 TMCO1 transmembrane and coiled-coil domains 1 123016 TTC8 tetratricopeptide repeat domain 8 51364 ZMYND10 zinc finger MYND-type containing 10 11179 ZNF277 zinc finger protein 277

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 7.57e-01 8.65e-30 GO ER membrane protein complex cellular_component 4.08e-01 2.70e-19 GO BBSome cellular_component 1.53e-01 2.49e-20 Reactome BBSome-mediated cargo-targeting to cilium Organelle biogenesis and maintenance

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 cilium organization 0.00e+00 0.00e+00 integral component of endoplasmic reticulum membrane 0.00e+00 0.00e+00 ER membrane protein complex 0.00e+00 0.00e+00 intrinsic component of endoplasmic reticulum membrane 0.00e+00 0.00e+00 BBSome 1.86e-12 1.28e-09 RNA polymerase II repressing transcription factor binding 8.79e-12 7.93e-09 cilium assembly 1.05e-10 6.38e-08 repressing transcription factor binding 1.08e-10 8.93e-08 organelle assembly 1.73e-10 1.40e-07 cell projection assembly 5.44e-10 3.01e-07 RNA polymerase II transcription factor binding 5.73e-10 4.40e-07 protein folding in endoplasmic reticulum 2.57e-09 1.10e-06 ciliary membrane 4.58e-08 2.73e-05 protein localization to cilium 9.45e-07 4.52e-04 melanosome transport 9.51e-07 4.54e-04 pigment granule transport 9.51e-07 4.54e-04 establishment of melanosome localization 9.63e-07 4.59e-04 melanosome localization 1.22e-06 3.52e-04 ciliary basal body 2.27e-06 6.26e-04 cell projection membrane

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.87e-10 2.03e-05 retinal degeneration 8.52e-09 2.31e-04 obese 1.38e-06 1.12e-02 absent sperm flagellum 1.70e-06 1.30e-02 enlarged third ventricle 3.84e-06 2.36e-02 small hippocampus 5.64e-06 3.17e-02 decreased birth body size 3.23e-05 1.07e-01 thin cerebral cortex 3.48e-05 1.12e-01 enlarged lateral ventricles 4.86e-05 1.39e-01 increased food intake 6.32e-05 1.66e-01 photoreceptor inner segment degeneration 1.76e-04 3.24e-01 impaired olfaction 2.41e-04 3.93e-01 taste/olfaction phenotype 4.30e-04 5.55e-01 abnormal olfactory epithelium morphology 5.75e-04 6.59e-01 photoreceptor outer segment degeneration 1.06e-03 9.29e-01 retinal outer nuclear layer degeneration 1.87e-03 1.00e+00 increased basophil cell number 2.13e-03 1.00e+00 polyphagia 2.63e-03 1.00e+00 increased circulating leptin level 3.74e-03 1.00e+00 abnormal ependyma motile cilium morphology 5.61e-03 1.00e+00 increased circulating lactate dehydrogenase level

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

²FDR corrected p-value (Benjamini-Hochberg)