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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod346

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod346 Module size 52 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 14 AAMP angio associated migratory cell protein 100 ADA adenosine deaminase 23246 BOP1 block of proliferation 1 55299 BRIX1 BRX1, biogenesis of ribosomes 51490 C9orf114 SPOUT domain containing methyltransferase 1 51816 CECR1 adenosine deaminase 2 1662 DDX10 DEAD-box helicase 10 10521 DDX17 DEAD-box helicase 17 8886 DDX18 DEAD-box helicase 18 9188 DDX21 DExD-box helicase 21 1655 DDX5 DEAD-box helicase 5 79009 DDX50 DExD-box helicase 50 83479 DDX59 DEAD-box helicase 59 55601 DDX60 DExD/H-box helicase 60 27292 DIMT1 DIM1 dimethyladenosine transferase 1 homolog 1736 DKC1 dyskerin pseudouridine synthase 1 64118 DUS1L dihydrouridine synthase 1 like 60528 ELAC2 elaC ribonuclease Z 2 2091 FBL fibrillarin 54552 GNL3L G protein nucleolar 3 like 83743 GRWD1 glutamate rich WD repeat containing 1 55027 HEATR3 HEAT repeat containing 3 92856 IMP4 IMP4, U3 small nucleolar ribonucleoprotein 54758 KLHDC4 kelch domain containing 4 23367 LARP1 La ribonucleoprotein domain family member 1 23195 MDN1 midasin AAA ATPase 1 84365 MKI67IP nucleolar protein interacting with the FHA domain of MKI67 92345 NAF1 nuclear assembly factor 1 ribonucleoprotein 51388 NIP7 NIP7, nucleolar pre-rRNA processing protein 310512 NMD3 NMD3 ribosome export adaptor 9221 NOLC1 nucleolar and coiled-body phosphoprotein 1 4839 NOP2 NOP2 nucleolar protein 10528 NOP56 NOP56 ribonucleoprotein 51602 NOP58 NOP58 ribonucleoprotein 5036 PA2G4 proliferation-associated 2G4 5134 PDCD2 programmed cell death 2 56902 PNO1 partner of NOB1 homolog 10623 POLR3C RNA polymerase III subunit C 10196 PRMT3 protein arginine methyltransferase 3 55170 PRMT6 protein arginine methyltransferase 6 56341 PRMT8 protein arginine methyltransferase 8 5670 PSG2 pregnancy specific beta-1-glycoprotein 2 297784 RRS1 ribosome biogenesis regulator homolog 6499 SKIV2L Ski2 like RNA helicase 51106 TFB1M transcription factor B1, mitochondrial 64216 TFB2M transcription factor B2, mitochondrial 55687 TRMT1 tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase 142940 TRUB1 TruB pseudouridine synthase family member 1 9875 URB1 URB1 ribosome biogenesis homolog 55759 WDR12 WD repeat domain 12 90441 ZNF622 zinc finger protein 622 30834 ZNRD1 zinc ribbon domain containing 1

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 2.83e-01 1.71e-09 GO box C/D snoRNP complex cellular_component 1.22e-01 2.27e-06 GO RNA helicase activity molecular_function 1.05e-01 3.46e-08 GO rRNA methylation biological_process 9.14e-02 1.07e-06 GO peptidyl-arginine methylation, to asymmetrical-dimethyl arginine biological_process 9.11e-02 2.27e-06 GO ribosomal large subunit export from nucleus biological_process 9.05e-02 1.07e-06 GO protein-arginine omega-N asymmetric methyltransferase activity molecular_function 8.31e-02 5.47e-03 Reactome Telomere Extension By Telomerase Cell Cycle 7.61e-02 7.29e-05 GO PeBoW complex cellular_component 7.39e-02 1.59e-06 GO small nucleolar ribonucleoprotein complex cellular_component 7.32e-02 1.09e-10 GO ribosomal large subunit biogenesis biological_process 4.51e-02 1.39e-08 GO ribosomal large subunit assembly biological_process 3.90e-02 4.00e-09 GO preribosome, large subunit precursor cellular_component 2.99e-02 7.29e-05 GO box H/ACA snoRNP complex cellular_component 2.32e-02 7.29e-05 GO box H/ACA snoRNA binding molecular_function 1.74e-02 3.25e-04 GO pseudouridine synthase activity molecular_function 1.53e-02 2.85e-05 GO ATP-dependent RNA helicase activity molecular_function 9.55e-03 1.28e-15 GO rRNA processing biological_process 1.11e-03 4.19e-07 GO snoRNA binding molecular_function

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 rRNA modification 0.00e+00 0.00e+00 rRNA metabolic process 0.00e+00 0.00e+00 ribosomal large subunit biogenesis 0.00e+00 0.00e+00 RNA modification 0.00e+00 0.00e+00 ribosome biogenesis 0.00e+00 0.00e+00 ribonucleoprotein complex biogenesis 0.00e+00 0.00e+00 rRNA processing 0.00e+00 0.00e+00 intracellular ribonucleoprotein complex 0.00e+00 0.00e+00 ribonucleoprotein complex 1.35e-11 7.49e-09 preribosome, large subunit precursor 3.04e-10 1.76e-07 methyltransferase activity 3.08e-10 1.78e-07 N-methyltransferase activity 4.51e-10 2.53e-07 S-adenosylmethionine-dependent methyltransferase activity 9.58e-10 7.16e-07 RNA secondary structure unwinding 1.49e-09 7.67e-07 rRNA methyltransferase activity 3.43e-09 1.44e-06 small nucleolar ribonucleoprotein complex 9.66e-09 4.42e-06 ATP-dependent RNA helicase activity 1.01e-08 4.60e-06 RNA-dependent ATPase activity 1.13e-08 5.11e-06 RNA helicase activity 1.72e-08 1.09e-05 methylation

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.41e-03 1.36e-01 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 3.44e-03 3.35e-01 PURINE SALVAGE 5.27e-03 4.77e-01 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 9.19e-03 6.85e-01 TRANSCRIPTION 1.02e-02 7.44e-01 EXTENSION OF TELOMERES 1.03e-02 7.50e-01 TELOMERE MAINTENANCE 1.19e-02 9.15e-01 EXTENSION OF TELOMERES 1.54e-02 1.00e+00 TELOMERE MAINTENANCE 1.66e-02 1.00e+00 PURINE SALVAGE 2.15e-02 1.00e+00 RNA POL III CHAIN ELONGATION 2.15e-02 1.00e+00 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 2 PROMOTER 2.15e-02 1.00e+00 RNA POL III TRANSCRIPTION TERMINATION 2.15e-02 1.00e+00 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 3 PROMOTER 2.16e-02 1.00e+00 RNA POL III TRANSCRIPTION 2.38e-02 1.00e+00 RNA POL III CHAIN ELONGATION 2.38e-02 1.00e+00 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 2 PROMOTER 2.49e-02 1.00e+00 PURINE METABOLISM 2.54e-02 1.00e+00 TRANSCRIPTION 2.70e-02 1.00e+00 RNA POL III TRANSCRIPTION TERMINATION 2.72e-02 1.00e+00 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 3 PROMOTER

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.65e-04 3.13e-01 decreased fibroblast proliferation 1.31e-03 1.00e+00 increased fibroblast apoptosis 1.86e-03 1.00e+00 early cellular replicative senescence 1.98e-03 1.00e+00 abnormal vascular development 3.77e-03 1.00e+00 increased renal carcinoma incidence 3.77e-03 1.00e+00 decreased hematopoietic stem cell proliferation 5.51e-03 1.00e+00 abnormal pulmonary alveolus morphology 5.62e-03 1.00e+00 abnormal penile erection 5.88e-03 1.00e+00 embryonic growth arrest 7.08e-03 1.00e+00 decreased bone mineral content 7.41e-03 1.00e+00 extramedullary hematopoiesis 7.50e-03 1.00e+00 intrahepatic cholestasis 7.93e-03 1.00e+00 decreased T cell number 9.39e-03 1.00e+00 pulmonary interstitial fibrosis 1.12e-02 1.00e+00 decreased cranium length 1.12e-02 1.00e+00 decreased areal bone mineral density 1.12e-02 1.00e+00 abnormal pulmonary alveolar parenchyma morphology 1.31e-02 1.00e+00 priapism 1.31e-02 1.00e+00 absent heart 1.50e-02 1.00e+00 increased fibrosarcoma incidence

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

²FDR corrected p-value (Benjamini-Hochberg)