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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod287

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod287 Module size 42 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 57448 BIRC6 baculoviral IAP repeat containing 6 136895 C7orf31 chromosome 7 open reading frame 31 200014 CC2D1B coiled-coil and C2 domain containing 1B 881 CCIN calicin 8452 CUL3 cullin 3 10072 DPP3 dipeptidyl peptidase 3 9920 KBTBD11 kelch repeat and BTB domain containing 11 166348 KBTBD12 kelch repeat and BTB domain containing 12 390594 KBTBD13 kelch repeat and BTB domain containing 13 25948 KBTBD2 kelch repeat and BTB domain containing 2 55709 KBTBD4 kelch repeat and BTB domain containing 4 131377 KBTBD5 kelch like family member 40 84541 KBTBD8 kelch repeat and BTB domain containing 8 200845 KCTD6 potassium channel tetramerization domain containing 6 127707 KLHDC7A kelch domain containing 7A 113730 KLHDC7B kelch domain containing 7B 57626 KLHL1 kelch like family member 1 317719 KLHL10 kelch like family member 10 57565 KLHL14 kelch like family member 14 151230 KLHL23 kelch like family member 23 55295 KLHL26 kelch like family member 26 114818 KLHL29 kelch like family member 29 377007 KLHL30 kelch like family member 30 401265 KLHL31 kelch like family member 31 114792 KLHL32 kelch like family member 32 257240 KLHL34 kelch like family member 34 283212 KLHL35 kelch like family member 35 79786 KLHL36 kelch like family member 36 340359 KLHL38 kelch like family member 38 56062 KLHL4 kelch like family member 4 51088 KLHL5 kelch like family member 5 89857 KLHL6 kelch like family member 6 23386 NUDCD3 NudC domain containing 3 284352 PPP1R37 protein phosphatase 1 regulatory subunit 37 391002 PRAMEF8 PRAME family member 8 49855 SCAPER S-phase cyclin A associated protein in the ER 9819 TSC22D2 TSC22 domain family member 2 63893 UBE2O ubiquitin conjugating enzyme E2 O 23078 VWA8 von Willebrand factor A domain containing 8 653067 XAGE1C X antigen family member 1B 79698 ZMAT4 zinc finger matrin-type 4 116225 ZMYND19 zinc finger MYND-type containing 19

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 6.02e-04 3.92e-06 GO protein monoubiquitination 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 protein modification by small protein conjugation 0.00e+00 0.00e+00 protein ubiquitination 0.00e+00 0.00e+00 transferase complex 0.00e+00 0.00e+00 ubiquitin ligase complex 0.00e+00 0.00e+00 cullin-RING ubiquitin ligase complex 0.00e+00 0.00e+00 Cul3-RING ubiquitin ligase complex 0.00e+00 0.00e+00 ubiquitin-protein transferase activity 0.00e+00 0.00e+00 ubiquitin-like protein transferase activity 1.99e-08 1.25e-05 protein ubiquitination involved in ubiquitin-dependent protein catabolic process 7.27e-06 2.90e-03 ubiquitin-dependent protein catabolic process 8.75e-06 3.43e-03 modification-dependent protein catabolic process 1.35e-05 5.06e-03 proteolysis involved in cellular protein catabolic process 1.57e-05 5.79e-03 cellular protein catabolic process 3.18e-05 1.08e-02 protein catabolic process 3.21e-04 7.78e-02 male gonad development 4.02e-04 9.36e-02 fertilization 4.65e-04 1.05e-01 spermatid development 5.43e-04 1.20e-01 male sex differentiation 5.79e-04 1.26e-01 spermatid differentiation 5.81e-04 1.27e-01 protein monoubiquitination

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 8.46e-04 1.02e-01 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 1.43e-03 1.60e-01 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 8.84e-03 6.65e-01 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 9.11e-03 6.80e-01 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.39e-03 1e+00 abnormal cell cycle 1.87e-03 1e+00 intraventricular hemorrhage 7.48e-03 1e+00 decreased germ cell number 7.48e-03 1e+00 increased immature B cell number 7.49e-03 1e+00 increased fibroblast apoptosis 9.34e-03 1e+00 increased thymocyte apoptosis 9.35e-03 1e+00 abnormal spongiotrophoblast layer morphology 1.12e-02 1e+00 decreased hepatocyte number 1.12e-02 1e+00 abnormal trophectoderm morphology 1.12e-02 1e+00 abnormal extraembryonic ectoderm morphology 1.12e-02 1e+00 abnormal lymph node germinal center morphology 1.30e-02 1e+00 abnormal adaptive immunity 1.31e-02 1e+00 abnormal placenta vasculature 1.31e-02 1e+00 decreased follicular B cell number 1.67e-02 1e+00 disorganized extraembryonic tissue 1.67e-02 1e+00 absent amnion 2.04e-02 1e+00 abnormal embryonic hematopoiesis 2.59e-02 1e+00 abnormal trophoblast giant cells 2.60e-02 1e+00 abnormal trophoblast layer morphology 2.60e-02 1e+00 decreased spleen weight

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

²FDR corrected p-value (Benjamini-Hochberg)