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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod319

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod319 Module size 76 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 54467 ANKIB1 ankyrin repeat and IBR domain containing 1 25820 ARIH1 ariadne RBR E3 ubiquitin protein ligase 1 10425 ARIH2 ariadne RBR E3 ubiquitin protein ligase 2 51283 BFAR bifunctional apoptosis regulator 23113 CUL9 cullin 9 55070 DET1 DET1, COP1 ubiquitin ligase partner 196403 DTX3 deltex E3 ubiquitin ligase 3 9666 DZIP3 DAZ interacting zinc finger protein 3 23285 KIAA1107 KIAA1107 158358 KIAA2026 KIAA2026 54708 MARCH5 membrane associated ring-CH-type finger 5 4281 MID1 midline 1 11043 MID2 midline 2 7681 MKRN3 makorin ring finger protein 3 79594 MUL1 mitochondrial E3 ubiquitin protein ligase 1 29116 MYLIP myosin regulatory light chain interacting protein 55611 OTUB1 OTU deubiquitinase, ubiquitin aldehyde binding 1 10616 RBCK1 RANBP2-type and C3HC4-type zinc finger containing 1 55159 RFWD3 ring finger and WD repeat domain 3 26994 RNF11 ring finger protein 11 55905 RNF114 ring finger protein 114 27246 RNF115 ring finger protein 115 54941 RNF125 ring finger protein 125 11342 RNF13 ring finger protein 13 51444 RNF138 ring finger protein 138 9604 RNF14 ring finger protein 14 50862 RNF141 ring finger protein 141 9781 RNF144A ring finger protein 144A 255488 RNF144B ring finger protein 144B 146310 RNF151 ring finger protein 151 220441 RNF152 ring finger protein 152 115992 RNF166 ring finger protein 166 26001 RNF167 ring finger protein 167 91445 RNF185 ring finger protein 185 25897 RNF19A ring finger protein 19A, RBR E3 ubiquitin protein ligase 127544 RNF19B ring finger protein 19B 154214 RNF217 ring finger protein 217 55182 RNF220 ring finger protein 220 64320 RNF25 ring finger protein 25 79102 RNF26 ring finger protein 26 6048 RNF5 ring finger protein 5 89970 RSPRY1 ring finger and SPRY domain containing 1 113938 SNURF SNRPN upstream reading frame 10273 STUB1 STIP1 homology and U-box containing protein 1 23321 TRIM2 tripartite motif containing 2 7706 TRIM25 tripartite motif containing 25 23087 TRIM35 tripartite motif containing 35 10475 TRIM38 tripartite motif containing 38 80263 TRIM45 tripartite motif containing 45 80128 TRIM46 tripartite motif containing 46 135892 TRIM50 tripartite motif containing 50 201292 TRIM65 tripartite motif containing 65 81603 TRIM8 tripartite motif containing 8 7317 UBA1 ubiquitin like modifier activating enzyme 1 7319 UBE2A ubiquitin conjugating enzyme E2 A 7320 UBE2B ubiquitin conjugating enzyme E2 B 7321 UBE2D1 ubiquitin conjugating enzyme E2 D1 7322 UBE2D2 ubiquitin conjugating enzyme E2 D2 7323 UBE2D3 ubiquitin conjugating enzyme E2 D3 51619 UBE2D4 ubiquitin conjugating enzyme E2 D4 (putative) 7325 UBE2E2 ubiquitin conjugating enzyme E2 E2 10477 UBE2E3 ubiquitin conjugating enzyme E2 E3 7332 UBE2L3 ubiquitin conjugating enzyme E2 L3 9246 UBE2L6 ubiquitin conjugating enzyme E2 L6 7334 UBE2N ubiquitin conjugating enzyme E2 N 389898 UBE2NL ubiquitin conjugating enzyme E2 N like (gene/pseudogene) 55585 UBE2Q1 ubiquitin conjugating enzyme E2 Q1 148581 UBE2U ubiquitin conjugating enzyme E2 U 55284 UBE2W ubiquitin conjugating enzyme E2 W 130507 UBR3 ubiquitin protein ligase E3 component n-recognin 3 51366 UBR5 ubiquitin protein ligase E3 component n-recognin 5 80019 UBTD1 ubiquitin domain containing 1 90850 ZNF598 zinc finger protein 598 84937 ZNRF1 zinc and ring finger 1 223082 ZNRF2 zinc and ring finger 2 148066 ZNRF4 zinc and ring finger 4

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 1.57e-01 1.82e-17 GO ubiquitin conjugating enzyme binding molecular_function 1.46e-01 1.67e-26 GO ubiquitin conjugating enzyme activity molecular_function 9.41e-02 4.05e-27 GO protein K48-linked ubiquitination biological_process 8.28e-02 3.34e-07 GO negative regulation of viral release from host cell biological_process 6.17e-02 1.33e-20 GO protein K63-linked ubiquitination biological_process 5.59e-02 9.21e-20 GO protein autoubiquitination biological_process 5.52e-02 1.82e-17 GO protein K11-linked ubiquitination biological_process 4.87e-02 1.50e-27 GO ubiquitin ligase complex cellular_component 3.76e-02 4.78e-15 GO positive regulation of proteasomal ubiquitin-dependent protein catabolic process biological_process 3.53e-02 2.72e-10 GO transferase activity molecular_function 2.45e-02 4.56e-41 Reactome Antigen processing: Ubiquitination & Proteasome degradation Immune System 2.13e-02 1.22e-02 GO protein linear polyubiquitination biological_process 1.55e-02 3.90e-09 Reactome Interferon gamma signaling Immune System 1.22e-02 7.21e-04 GO protein localization to microtubule biological_process 1.07e-02 1.40e-12 Reactome E3 ubiquitin ligases ubiquitinate target proteins Metabolism of proteins 9.61e-03 4.53e-09 Reactome Negative regulators of DDX58/IFIH1 signaling Immune System

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 0e+00 0e+00 proteolysis involved in cellular protein catabolic process 0e+00 0e+00 protein modification by small protein conjugation 0e+00 0e+00 protein ubiquitination 0e+00 0e+00 cellular protein catabolic process 0e+00 0e+00 modification-dependent protein catabolic process 0e+00 0e+00 protein autoubiquitination 0e+00 0e+00 protein K11-linked ubiquitination 0e+00 0e+00 protein K48-linked ubiquitination 0e+00 0e+00 protein polyubiquitination 0e+00 0e+00 protein catabolic process 0e+00 0e+00 ubiquitin-dependent protein catabolic process 0e+00 0e+00 protein ubiquitination involved in ubiquitin-dependent protein catabolic process 0e+00 0e+00 protein K63-linked ubiquitination 0e+00 0e+00 regulation of proteasomal protein catabolic process 0e+00 0e+00 positive regulation of proteasomal protein catabolic process 0e+00 0e+00 positive regulation of proteasomal ubiquitin-dependent protein catabolic process 0e+00 0e+00 regulation of proteasomal ubiquitin-dependent protein catabolic process 0e+00 0e+00 ubiquitin ligase complex 0e+00 0e+00 ubiquitin-protein transferase activity 0e+00 0e+00 ubiquitin conjugating enzyme activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 0.00e+00 0.00e+00 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 0.00e+00 0.00e+00 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 0.00e+00 0.00e+00 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 3.58e-10 1.23e-07 NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING 9.73e-10 2.38e-07 NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING 6.07e-08 1.61e-05 RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS 8.52e-07 1.50e-04 RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS 1.52e-05 2.82e-03 INNATE IMMUNE SYSTEM 1.59e-05 2.93e-03 OXYGEN DEPENDENT PROLINE HYDROXYLATION OF HYPOXIA INDUCIBLE FACTOR ALPHA 6.80e-05 1.10e-02 REGULATION OF HYPOXIA INDUCIBLE FACTOR HIF BY OXYGEN 9.11e-05 1.43e-02 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 1.14e-04 1.43e-02 INNATE IMMUNE SYSTEM 1.50e-04 1.83e-02 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 2.40e-04 2.80e-02 OXYGEN DEPENDENT PROLINE HYDROXYLATION OF HYPOXIA INDUCIBLE FACTOR ALPHA 4.48e-04 4.91e-02 REGULATION OF HYPOXIA INDUCIBLE FACTOR HIF BY OXYGEN 8.29e-04 9.99e-02 SIGNALING BY TGF BETA RECEPTOR COMPLEX 1.21e-03 1.39e-01 DOWNREGULATION OF SMAD2 3 SMAD4 TRANSCRIPTIONAL ACTIVITY 1.37e-03 1.33e-01 SIGNALING BY TGF BETA RECEPTOR COMPLEX 2.00e-03 1.86e-01 INTERFERON SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.75e-03 1e+00 increased pituitary gland tumor incidence 7.48e-03 1e+00 tau protein deposits 7.48e-03 1e+00 small pharyngeal arch 7.49e-03 1e+00 increased stomach pH 9.34e-03 1e+00 partial embryonic lethality at implantation 9.34e-03 1e+00 abnormal cerebellum deep nucleus morphology 9.34e-03 1e+00 anosmia 9.35e-03 1e+00 retinal ganglion cell degeneration 9.35e-03 1e+00 decreased follicle stimulating hormone level 1.12e-02 1e+00 hypochlorhydria 1.31e-02 1e+00 increased bone strength 1.31e-02 1e+00 decreased circulating prolactin level 1.31e-02 1e+00 increased ovary tumor incidence 1.43e-02 1e+00 ataxia 1.49e-02 1e+00 abnormal chiasmata formation 1.50e-02 1e+00 thymus atrophy 1.66e-02 1e+00 small uterus 1.68e-02 1e+00 delayed female fertility 1.84e-02 1e+00 decreased cellular sensitivity to ultraviolet irradiation 1.86e-02 1e+00 prolonged diestrus

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

²FDR corrected p-value (Benjamini-Hochberg)