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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod300

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod300 Module size 54 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 9582 APOBEC3B apolipoprotein B mRNA editing enzyme catalytic subunit 3B 28987 ART4 NIN1 (RPN12) binding protein 1 homolog 10974 C10orf116 adipogenesis regulatory factor 144535 C12orf55 cilia and flagella associated protein 54 100170841 C17orf96 elongin BC and polycomb repressive complex 2 associated protein 55286 C4orf19 chromosome 4 open reading frame 19 51244 CCDC174 coiled-coil domain containing 174 80323 CCDC68 coiled-coil domain containing 68 8872 CDC123 cell division cycle 123 688 CKLF Kruppel like factor 5 159013 CXorf38 chromosome X open reading frame 38 1939 EIF2D eukaryotic translation initiation factor 2D 728689 EIF3CL eukaryotic translation initiation factor 3 subunit C like 63901 FAM111A family with sequence similarity 111 member A 26071 FAM127B retrotransposon Gag like 8A 130074 FAM168B family with sequence similarity 168 member B 51031 GLOD4 glyoxalase domain containing 4 2843 GPR20 G protein-coupled receptor 20 10149 GPR64 adhesion G protein-coupled receptor G2 112802 KRT71 keratin 71 619373 MBOAT4 membrane bound O-acyltransferase domain containing 4 100462977 MTRNR2L1 MT-RNR2 like 1 65065 NBEAL1 neurobeachin like 1 23218 NBEAL2 neurobeachin like 2 10397 NDRG1 N-myc downstream regulated 1 54729 NKX1-1 NK1 homeobox 1 28989 NTMT1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 51247 PAIP2 poly(A) binding protein interacting protein 2 400961 PAIP2B poly(A) binding protein interacting protein 2B 8505 PARG poly(ADP-ribose) glycohydrolase 64081 PBLD phenazine biosynthesis like protein domain containing 26499 PLEK2 pleckstrin 2 5518 PPP2R1A protein phosphatase 2 scaffold subunit Aalpha 5520 PPP2R2A protein phosphatase 2 regulatory subunit Balpha 5619 PRM1 protamine 1 23627 PRND prion like protein doppel 253143 PRR14L proline rich 14 like 53635 PTOV1 prostate tumor overexpressed 1 6233 RPS27A ribosomal protein S27a 57515 SERINC1 serine incorporator 1 23049 SMG1 SMG1, nonsense mediated mRNA decay associated PI3K related kinase 27044 SND1 staphylococcal nuclease and tudor domain containing 1 79689 STEAP4 STEAP4 metalloreductase 7015 TERT telomerase reverse transcriptase 79073 TMEM109 transmembrane protein 109 79989 TTC26 tetratricopeptide repeat domain 26 79770 TXNDC15 thioredoxin domain containing 15 7311 UBA52 ubiquitin A-52 residue ribosomal protein fusion product 1 6233 UBC ribosomal protein S27a 143630 UBQLNL ubiquilin like 84305 WIBG PYM homolog 1, exon junction complex associated factor 24883 WT1 Wilms tumor 1 84240 ZCCHC9 zinc finger CCHC-type containing 9 27309 ZNF330 zinc finger protein 330

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 1.19e-01 4.54e-03 Reactome Telomere Extension By Telomerase Cell Cycle 7.14e-02 2.23e-08 Reactome Spry regulation of FGF signaling Signal Transduction 5.75e-02 6.01e-07 Reactome Downregulation of ERBB4 signaling Signal Transduction 5.74e-02 6.01e-07 Reactome Regulation of PTEN localization Signal Transduction 2.83e-02 9.01e-07 Reactome PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 Signal Transduction 2.18e-02 1.28e-06 Reactome IRAK2 mediated activation of TAK1 complex Immune System 1.13e-02 1.28e-06 Reactome InlA-mediated entry of Listeria monocytogenes into host cells Disease 1.08e-02 1.28e-06 Reactome Glycogen storage diseases Disease 8.61e-03 1.28e-06 Reactome Diseases of carbohydrate metabolism Disease 8.10e-03 1.76e-06 GO virion assembly biological_process 8.10e-03 1.76e-06 GO protein tag molecular_function 8.08e-03 1.76e-06 GO intracellular transport of virus biological_process 4.45e-03 1.28e-06 Reactome Myoclonic epilepsy of Lafora Disease 1.37e-03 4.49e-04 GO negative regulation of translational initiation 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 2.40e-06 1.06e-03 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 8.42e-06 3.32e-03 RNA catabolic process 2.33e-05 8.22e-03 G2/M transition of mitotic cell cycle 2.34e-05 8.25e-03 cell cycle G2/M phase transition 3.01e-05 1.03e-02 nucleotide-excision repair, DNA duplex unwinding 3.51e-05 1.18e-02 endoplasmic reticulum mannose trimming 4.07e-05 1.34e-02 nucleotide-excision repair, preincision complex assembly 4.64e-05 1.50e-02 protein alpha-1,2-demannosylation 4.69e-05 1.52e-02 nucleotide-excision repair, DNA gap filling 5.34e-05 1.70e-02 error-free translesion synthesis 5.88e-05 1.85e-02 nucleotide-excision repair, DNA damage recognition 6.11e-05 1.90e-02 nuclear-transcribed mRNA catabolic process 6.12e-05 1.91e-02 global genome nucleotide-excision repair 6.65e-05 2.05e-02 error-prone translesion synthesis 6.65e-05 1.38e-02 endoplasmic reticulum quality control compartment 6.92e-05 2.12e-02 signal transduction by p53 class mediator 6.94e-05 2.13e-02 entry of bacterium into host cell 6.97e-05 2.14e-02 mRNA catabolic process 1.02e-04 2.97e-02 glycogen biosynthetic process 1.06e-04 3.07e-02 mitotic nuclear envelope reassembly

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 6.33e-07 1.14e-04 NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX 1.73e-06 2.90e-04 G1 PHASE 2.29e-06 4.85e-04 NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX 4.76e-06 9.57e-04 G1 PHASE 1.78e-05 2.57e-03 SPRY REGULATION OF FGF SIGNALING 2.02e-05 3.65e-03 SPRY REGULATION OF FGF SIGNALING 5.92e-05 7.85e-03 METABOLISM OF MRNA 7.59e-05 1.21e-02 MEMBRANE BINDING AND TARGETTING OF GAG PROTEINS 8.52e-05 1.34e-02 METABOLISM OF MRNA 1.03e-04 1.31e-02 RECEPTOR LIGAND BINDING INITIATES THE SECOND PROTEOLYTIC CLEAVAGE OF NOTCH RECEPTOR 1.23e-04 1.87e-02 ACTIVATION OF IRF3 IRF7 MEDIATED BY TBK1 IKK EPSILON 1.65e-04 1.99e-02 REGULATION OF THE FANCONI ANEMIA PATHWAY 1.77e-04 2.12e-02 MEMBRANE BINDING AND TARGETTING OF GAG PROTEINS 1.82e-04 2.64e-02 APC CDC20 MEDIATED DEGRADATION OF NEK2A 1.84e-04 2.20e-02 ACTIVATION OF IRF3 IRF7 MEDIATED BY TBK1 IKK EPSILON 1.93e-04 2.29e-02 METABOLISM OF RNA 1.99e-04 2.36e-02 TGF BETA RECEPTOR SIGNALING IN EMT EPITHELIAL TO MESENCHYMAL TRANSITION 2.18e-04 3.10e-02 REGULATION OF THE FANCONI ANEMIA PATHWAY 2.45e-04 3.43e-02 METABOLISM OF RNA 3.02e-04 3.45e-02 DOWNREGULATION OF ERBB2 ERBB3 SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.36e-04 6.97e-01 decreased thymocyte apoptosis 7.41e-04 7.61e-01 decreased cell proliferation 2.47e-03 1.00e+00 abnormal liver development 5.13e-03 1.00e+00 early cellular replicative senescence 5.62e-03 1.00e+00 prognathia 6.80e-03 1.00e+00 increased lung adenocarcinoma incidence 7.47e-03 1.00e+00 decreased circulating ghrelin level 7.80e-03 1.00e+00 abnormal spermiogenesis 9.33e-03 1.00e+00 abnormal optic pit morphology 9.35e-03 1.00e+00 decreased liver tumor incidence 9.35e-03 1.00e+00 increased small intestinal crypt cell apoptosis 9.38e-03 1.00e+00 abnormal spleen development 9.38e-03 1.00e+00 abnormal kidney interlobular artery morphology 9.39e-03 1.00e+00 abnormal mesangial cell morphology 1.12e-02 1.00e+00 abnormal platelet shape 1.12e-02 1.00e+00 abnormal hair cortex morphology 1.12e-02 1.00e+00 absent podocyte foot process 1.12e-02 1.00e+00 myocardium hypoplasia 1.12e-02 1.00e+00 abnormal heart apex morphology 1.31e-02 1.00e+00 podocyte hypertrophy

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

²FDR corrected p-value (Benjamini-Hochberg)