Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod226

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod226 Module size 79 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 113146 AHNAK2 AHNAK nucleoprotein 2 56672 AKIP1 A-kinase interacting protein 1 55626 AMBRA1 autophagy and beclin 1 regulator 1 694 BTG1 BTG anti-proliferation factor 1 128864 C20orf144 chromosome 20 open reading frame 144 55832 CAND1 cullin associated and neddylation dissociated 1 23066 CAND2 cullin associated and neddylation dissociated 2 (putative) 8030 CCDC6 coiled-coil domain containing 6 60494 CCDC81 coiled-coil domain containing 81 997 CDC34 cell division cycle 34 11129 CLASRP CLK4 associating serine/arginine rich protein 8454 CUL1 cullin 1 8065 CUL5 cullin 5 285429 DCAF4L1 DDB1 and CUL4 associated factor 4 like 1 139425 DCAF8L1 DDB1 and CUL4 associated factor 8 like 1 54165 DCUN1D1 defective in cullin neddylation 1 domain containing 1 55208 DCUN1D2 defective in cullin neddylation 1 domain containing 2 123879 DCUN1D3 defective in cullin neddylation 1 domain containing 3 23142 DCUN1D4 defective in cullin neddylation 1 domain containing 4 84259 DCUN1D5 defective in cullin neddylation 1 domain containing 5 54749 EPDR1 ependymin related 1 80013 FAM188A MINDY lysine 48 deubiquitinase 3 54850 FBXL12 F-box and leucine rich repeat protein 12 222235 FBXL13 F-box and leucine rich repeat protein 13 25827 FBXL2 F-box and leucine rich repeat protein 2 84961 FBXL20 F-box and leucine rich repeat protein 20 55336 FBXL8 F-box and leucine rich repeat protein 8 26267 FBXO10 F-box protein 10 80204 FBXO11 F-box protein 11 157574 FBXO16 F-box protein 16 26263 FBXO22 F-box protein 22 23219 FBXO28 F-box protein 28 26273 FBXO3 F-box protein 3 55294 FBXO30 F-box and WD repeat domain containing 7 114907 FBXO32 F-box protein 32 254170 FBXO33 F-box protein 33 150726 FBXO41 F-box protein 41 23403 FBXO46 F-box protein 46 285231 FBXW12 F-box and WD repeat domain containing 12 65991 FUNDC2 FUN14 domain containing 2 55364 IMPACT impact RWD domain protein 283219 KCTD21 potassium channel tetramerization domain containing 21 192666 KRT24 keratin 24 5428 MDP1 DNA polymerase gamma, catalytic subunit 150365 MEI1 meiotic double-stranded break formation protein 1 27304 MOCS3 molybdenum cofactor synthesis 3 83463 MXD3 MAX dimerization protein 3 8883 NAE1 NEDD8 activating enzyme E1 subunit 1 4738 NEDD8 neural precursor cell expressed, developmentally down-regulated 8 100528064 NEDD8-MDP1 NEDD8-MDP1 readthrough 57097 PARP11 poly(ADP-ribose) polymerase family member 11 23532 PRAME preferentially expressed antigen in melanoma 25797 QPCT glutaminyl-peptide cyclotransferase 9978 RBX1 ring-box 1 123228 SENP8 SUMO peptidase family member, NEDD8 specific 27244 SESN1 sestrin 1 6500 SKP1 S-phase kinase associated protein 1 128710 SLX4IP SLX4 interacting protein 219793 TBATA thymus, brain and testes associated 79178 THTPA thiamine triphosphatase 100910678 TMA7 coiled-coil domain-containing protein 72-like 23671 TMEFF2 transmembrane protein with EGF like and two follistatin like domains 2 1861 TOR1A torsin family 1 member A 27348 TOR1B torsin family 1 member B 7260 TSSC1 EARP complex and GARP complex interacting protein 1 9039 UBA3 ubiquitin like modifier activating enzyme 3 79876 UBA5 ubiquitin like modifier activating enzyme 5 7318 UBA7 ubiquitin like modifier activating enzyme 7 140739 UBE2F ubiquitin conjugating enzyme E2 F (putative) 9040 UBE2M ubiquitin conjugating enzyme E2 M 7345 UCHL1 ubiquitin C-terminal hydrolase L1 81605 URM1 ubiquitin related modifier 1 27005 USP16 ubiquitin specific peptidase 21 10868 USP20 ubiquitin specific peptidase 20 84196 USP31 ubiquitin specific peptidase 48 9730 VPRBP DDB1 and CUL4 associated factor 1 51530 ZC3HC1 zinc finger C3HC-type containing 1 10444 ZER1 zyg-11 related cell cycle regulator 79699 ZYG11B zyg-11 family member B, cell cycle regulator

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 5.86e-01 8.69e-26 GO protein neddylation biological_process 8.38e-02 5.39e-07 Reactome FBXW7 Mutants and NOTCH1 in Cancer Disease 7.76e-02 5.39e-07 Reactome Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling Disease 4.19e-02 1.30e-15 GO cullin family protein binding molecular_function 3.20e-02 1.41e-33 Reactome Neddylation Metabolism of proteins 3.06e-02 6.42e-04 GO cellular response to leucine starvation biological_process 2.64e-02 8.06e-13 GO SCF ubiquitin ligase complex cellular_component 1.73e-02 5.17e-11 GO cellular protein modification process biological_process 1.34e-02 2.14e-12 GO SCF-dependent proteasomal ubiquitin-dependent protein catabolic process biological_process 7.40e-03 9.62e-08 GO cullin-RING ubiquitin ligase complex cellular_component 4.46e-03 1.72e-22 Reactome Antigen processing: Ubiquitination & Proteasome degradation 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 0.00e+00 0.00e+00 protein neddylation 0.00e+00 0.00e+00 protein modification by small protein conjugation 0.00e+00 0.00e+00 protein polyubiquitination 0.00e+00 0.00e+00 ubiquitin ligase complex 3.01e-20 2.90e-17 protein ubiquitination 4.94e-17 3.48e-14 ubiquitin-protein transferase activity 1.09e-16 7.68e-14 ubiquitin-like protein transferase activity 1.22e-12 1.13e-09 proteolysis involved in cellular protein catabolic process 2.04e-12 1.88e-09 modification-dependent protein catabolic process 2.09e-12 1.43e-09 cullin family protein binding 2.59e-12 2.38e-09 cellular protein catabolic process 1.47e-11 1.31e-08 protein catabolic process 2.01e-11 1.78e-08 ubiquitin-dependent protein catabolic process 3.45e-11 3.00e-08 SCF complex assembly 3.60e-11 3.12e-08 regulation of ubiquitin-protein transferase activity 2.25e-10 1.11e-07 transferase complex 6.48e-10 2.98e-07 cullin-RING ubiquitin ligase complex 2.07e-09 1.48e-06 regulation of protein ubiquitination 1.06e-08 6.87e-06 positive regulation of ubiquitin-protein transferase activity 2.04e-08 1.28e-05 positive regulation of protein ubiquitination

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 8.98e-06 1.74e-03 PROLACTIN RECEPTOR SIGNALING 1.33e-05 1.94e-03 PROLACTIN RECEPTOR SIGNALING 8.41e-05 1.33e-02 NUCLEAR SIGNALING BY ERBB4 9.81e-05 1.25e-02 NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION 1.86e-04 2.69e-02 NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION 2.50e-04 3.50e-02 IL1 SIGNALING 2.93e-04 3.36e-02 IL1 SIGNALING 3.13e-04 3.56e-02 NUCLEAR SIGNALING BY ERBB4 3.83e-04 4.27e-02 SIGNALING BY NOTCH1 5.86e-04 7.40e-02 SIGNALING BY NOTCH1 1.21e-03 1.19e-01 SIGNALING BY NOTCH 1.71e-03 1.86e-01 SIGNALING BY NOTCH 4.03e-03 3.82e-01 SIGNALING BY ERBB4 5.47e-03 4.41e-01 CYTOKINE SIGNALING IN IMMUNE SYSTEM 5.97e-03 4.77e-01 SIGNALING BY ERBB4 5.98e-03 4.77e-01 SIGNALING BY ILS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.53e-04 6.45e-01 decreased paired-pulse facilitation 2.89e-03 1.00e+00 abnormal female meiosis 3.75e-03 1.00e+00 abnormal thymus epithelium morphology 4.48e-03 1.00e+00 decreased grip strength 4.55e-03 1.00e+00 abnormal vocalization 6.77e-03 1.00e+00 neurodegeneration 7.12e-03 1.00e+00 complete embryonic lethality between implantation and placentation 7.48e-03 1.00e+00 abnormal external auditory canal morphology 7.48e-03 1.00e+00 decreased primordial ovarian follicle number 9.33e-03 1.00e+00 abnormal auditory tube 9.33e-03 1.00e+00 increased spinal cord size 9.33e-03 1.00e+00 increased embryonic neuroepithelial cell proliferation 9.34e-03 1.00e+00 abnormal dorsal striatum morphology 1.12e-02 1.00e+00 decreased red blood cell distribution width 1.16e-02 1.00e+00 arrest of male meiosis 1.29e-02 1.00e+00 increased startle reflex 1.31e-02 1.00e+00 increased lean body mass 1.31e-02 1.00e+00 decreased neurotransmitter release 1.49e-02 1.00e+00 absent embryonic epiblast 1.49e-02 1.00e+00 asymmetric snout

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

²FDR corrected p-value (Benjamini-Hochberg)