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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod197

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod197 Module size 18 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 79176 FBXL15 F-box and leucine rich repeat protein 15 26224 FBXL3 F-box and leucine rich repeat protein 3 26234 FBXL5 F-box and leucine rich repeat protein 5 23194 FBXL7 F-box and leucine rich repeat protein 7 201456 FBXO15 F-box protein 15 115290 FBXO17 F-box protein 17 26232 FBXO2 F-box protein 2 26260 FBXO25 F-box protein 25 126433 FBXO27 F-box protein 27 79791 FBXO31 F-box protein 31 26272 FBXO4 F-box protein 4 93611 FBXO44 F-box protein 44 26270 FBXO6 F-box protein 6 26268 FBXO9 F-box protein 9 54461 FBXW5 F-box and WD repeat domain containing 5 26259 FBXW8 F-box and WD repeat domain containing 8 222171 PRR15 proline rich 15 55031 USP47 ubiquitin specific peptidase 47

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 1.87e-01 3.61e-40 GO SCF ubiquitin ligase complex cellular_component 9.73e-03 2.81e-10 Reactome Association of TriC/CCT with target proteins during biosynthesis Metabolism of proteins

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 proteolysis involved in cellular protein catabolic process 0.00e+00 0.00e+00 proteasomal protein catabolic process 0.00e+00 0.00e+00 protein modification by small protein conjugation 0.00e+00 0.00e+00 proteasome-mediated ubiquitin-dependent protein catabolic process 0.00e+00 0.00e+00 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process 0.00e+00 0.00e+00 protein ubiquitination 0.00e+00 0.00e+00 cellular protein catabolic process 0.00e+00 0.00e+00 modification-dependent protein catabolic process 0.00e+00 0.00e+00 protein polyubiquitination 0.00e+00 0.00e+00 protein catabolic process 0.00e+00 0.00e+00 ubiquitin-dependent protein catabolic process 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 SCF ubiquitin ligase complex 0.00e+00 0.00e+00 ubiquitin-protein transferase activity 0.00e+00 0.00e+00 ubiquitin-like protein transferase activity 1.62e-06 4.96e-04 glycoprotein binding 2.01e-04 5.26e-02 glycoprotein catabolic process 5.10e-04 1.14e-01 negative regulation of mitotic cell cycle phase transition

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.68e-09 5.40e-07 ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS 5.16e-09 1.55e-06 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 7.45e-09 2.22e-06 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 2.71e-08 7.55e-06 PROTEIN FOLDING 3.47e-08 7.18e-06 ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS 7.43e-07 1.32e-04 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 9.30e-07 1.62e-04 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 9.57e-07 1.66e-04 PROTEIN FOLDING 2.24e-02 1.00e+00 CIRCADIAN CLOCK

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 abnormal circadian period 3.74e-03 1e+00 abnormal intestinal iron level 3.74e-03 1e+00 decreased liver iron level 3.74e-03 1e+00 cochlear degeneration 5.61e-03 1e+00 prolonged circadian period 5.61e-03 1e+00 abnormal brain size 5.61e-03 1e+00 increased hepatic hemangioma incidence 5.61e-03 1e+00 abnormal organ of Corti supporting cell morphology 7.46e-03 1e+00 abnormal Claudius cell morphology 7.47e-03 1e+00 abnormal iron level 7.47e-03 1e+00 abnormal extraembryonic tissue physiology 7.48e-03 1e+00 increased susceptibility to age-related hearing loss 9.32e-03 1e+00 increased uterus tumor incidence 9.33e-03 1e+00 degeneration of organ of Corti supporting cells 9.34e-03 1e+00 increased spleen iron level 9.35e-03 1e+00 abnormal iron homeostasis 1.12e-02 1e+00 increased hemangioma incidence 1.28e-02 1e+00 increased mammary gland tumor incidence 1.30e-02 1e+00 abnormal ectoplacental cone morphology 1.49e-02 1e+00 abnormal cochlear hair cell morphology

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

²FDR corrected p-value (Benjamini-Hochberg)