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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod102

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod102 Module size 40 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 53339 BTBD1 BTB domain containing 1 55643 BTBD2 BTB domain containing 2 9318 COPS2 COP9 signalosome subunit 2 8533 COPS3 COP9 signalosome subunit 3 51138 COPS4 COP9 signalosome subunit 4 10987 COPS5 COP9 signalosome subunit 5 10980 COPS6 COP9 signalosome subunit 6 50813 COPS7A COP9 signalosome subunit 7A 64708 COPS7B COP9 signalosome subunit 7B 10920 COPS8 COP9 signalosome subunit 8 51185 CRBN cereblon 1447 CSN2 casein beta 8533 CSN3 COP9 signalosome subunit 3 8451 CUL4A cullin 4A 8450 CUL4B cullin 4B 79269 DCAF10 DDB1 and CUL4 associated factor 10 80344 DCAF11 DDB1 and CUL4 associated factor 11 25853 DCAF12 DDB1 and CUL4 associated factor 12 90379 DCAF15 DDB1 and CUL4 associated factor 15 54876 DCAF16 DDB1 and CUL4 associated factor 16 80067 DCAF17 DDB1 and CUL4 associated factor 17 26094 DCAF4 DDB1 and CUL4 associated factor 4 8816 DCAF5 DDB1 and CUL4 associated factor 5 55827 DCAF6 DDB1 and CUL4 associated factor 6 10238 DCAF7 DDB1 and CUL4 associated factor 7 50717 DCAF8 DDB1 and CUL4 associated factor 8 688813 DDA1 DET1 and DDB1 associated 1 1642 DDB1 damage specific DNA binding protein 1 1643 DDB2 damage specific DNA binding protein 2 6468 FBXW4 F-box and WD repeat domain containing 4 2873 GPS1 G protein pathway suppressor 1 130535 KCTD18 potassium channel tetramerization domain containing 18 80311 KLHL15 kelch like family member 15 54800 KLHL24 kelch like family member 24 9684 LRRC14 leucine rich repeat containing 14 55023 PHIP pleckstrin homology domain interacting protein 9840 TESPA1 thymocyte expressed, positive selection associated 1 387357 THEMIS thymocyte selection associated 163590 TOR1AIP2 torsin 1A interacting protein 2 26133 TRPC4AP transient receptor potential cation channel subfamily C member 4 associated protein

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 5.33e-01 5.91e-24 GO protein deneddylation biological_process 4.09e-01 4.15e-37 GO Cul4-RING E3 ubiquitin ligase complex cellular_component 8.76e-02 5.06e-30 GO nucleotide-excision repair, DNA damage recognition biological_process 4.92e-02 1.10e-29 Reactome DNA Damage Recognition in GG-NER DNA Repair 3.29e-02 1.44e-21 GO COP9 signalosome cellular_component 4.39e-03 7.84e-38 Reactome Neddylation 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 protein ubiquitination 0.00e+00 0.00e+00 protein modification by small protein conjugation 0.00e+00 0.00e+00 DNA repair 0.00e+00 0.00e+00 transcription-coupled nucleotide-excision repair 0.00e+00 0.00e+00 nucleotide-excision repair 0.00e+00 0.00e+00 nucleotide-excision repair, DNA damage recognition 0.00e+00 0.00e+00 protein deneddylation 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 Cul4-RING E3 ubiquitin ligase complex 0.00e+00 0.00e+00 COP9 signalosome 5.11e-10 3.93e-07 cellular response to DNA damage stimulus 1.51e-09 1.10e-06 protein modification by small protein removal 4.43e-09 3.02e-06 DNA metabolic process 1.09e-08 7.06e-06 nucleotide-excision repair, DNA duplex unwinding 2.91e-08 1.78e-05 ubiquitin-dependent protein catabolic process 3.33e-08 2.02e-05 modification-dependent protein catabolic process 5.95e-08 2.13e-05 Cul4A-RING E3 ubiquitin ligase complex 6.51e-08 3.79e-05 nucleotide-excision repair, preincision complex assembly

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.00e-05 5.27e-03 FORMATION OF INCISION COMPLEX IN GG NER 3.07e-05 5.38e-03 GLOBAL GENOMIC NER GG NER 4.48e-05 7.58e-03 NUCLEOTIDE EXCISION REPAIR 9.22e-05 1.18e-02 FORMATION OF INCISION COMPLEX IN GG NER 9.45e-05 1.21e-02 GLOBAL GENOMIC NER GG NER 1.87e-04 2.23e-02 NUCLEOTIDE EXCISION REPAIR 8.74e-04 8.92e-02 DNA REPAIR 1.47e-03 1.64e-01 DNA REPAIR 5.58e-03 4.48e-01 NUCLEAR SIGNALING BY ERBB4 8.89e-03 6.68e-01 SIGNALING BY ERBB4 9.88e-03 7.93e-01 NUCLEAR SIGNALING BY ERBB4 9.94e-03 7.97e-01 SIGNALING BY ERBB4 3.74e-02 1.00e+00 ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 7.05e-05 1.79e-01 small thymus medulla 6.13e-04 6.83e-01 abnormal milk composition 7.57e-04 7.65e-01 increased memory T cell number 1.06e-03 9.29e-01 decreased regulatory T cell number 2.95e-03 1.00e+00 abnormal DNA repair 3.40e-03 1.00e+00 failure to gastrulate 4.57e-03 1.00e+00 abnormal T cell differentiation 5.61e-03 1.00e+00 partial lethality during fetal growth through weaning 5.61e-03 1.00e+00 abnormal dosage compensation, by inactivation of X chromosome 5.61e-03 1.00e+00 abnormal regulatory T cell morphology 5.62e-03 1.00e+00 abnormal eyelid aperture 7.58e-03 1.00e+00 decreased CD8-positive, alpha-beta T cell number 8.02e-03 1.00e+00 decreased CD4-positive, alpha beta T cell number 8.72e-03 1.00e+00 increased embryonic tissue cell apoptosis 9.33e-03 1.00e+00 abnormal trophoblast giant cell proliferation 9.34e-03 1.00e+00 decreased cellular sensitivity to ionizing radiation 9.34e-03 1.00e+00 increased incidence of tumors by UV-induction 1.12e-02 1.00e+00 abnormal hair cycle anagen phase 1.12e-02 1.00e+00 disorganized placental labyrinth 1.12e-02 1.00e+00 pale placenta

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

²FDR corrected p-value (Benjamini-Hochberg)