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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod90

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod90 Module size 58 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 26574 AATF apoptosis antagonizing transcription factor 29777 ABT1 activator of basal transcription 1 64782 AEN apoptosis enhancing nuclease 56647 BCCIP BRCA2 and CDKN1A interacting protein 84310 C7orf50 chromosome 7 open reading frame 50 84319 CMSS1 cms1 ribosomal small subunit homolog 55794 DDX28 DEAD-box helicase 28 51202 DDX47 DEAD-box helicase 47 54555 DDX49 DEAD-box helicase 49 30836 DNTTIP2 deoxynucleotidyltransferase terminal interacting protein 2 10969 EBNA1BP2 EBNA1 binding protein 2 51575 ESF1 ESF1 nucleolar pre-rRNA processing protein homolog 51236 FAM203A HGH1 homolog 51236 FAM203B HGH1 homolog 51077 FCF1 FCF1, rRNA-processing protein 29997 GLTSCR2 NOP53 ribosome biogenesis factor 81875 ISG20L2 interferon stimulated exonuclease gene 20 like 2 146212 KCTD19 potassium channel tetramerization domain containing 19 65095 KRI1 KRI1 homolog 11103 KRR1 KRR1, small subunit processome component homolog 55132 LARP1B La ribonucleoprotein domain family member 1B 51574 LARP7 La ribonucleoprotein domain family member 7 84946 LTV1 LTV1 ribosome biogenesis factor 55646 LYAR Ly1 antibody reactive 84549 MAK16 MAK16 homolog 25983 NGDN neuroguidin 28987 NOB1 NIN1 (RPN12) binding protein 1 homolog 79159 NOL12 nucleolar protein 12 84306 PDCD2L programmed cell death 2 like 54984 PINX1 PIN2 (TERF1) interacting telomerase inhibitor 1 56342 PPAN peter pan homolog 692312 PPAN-P2RY11 PPAN-P2RY11 readthrough 55131 RBM28 RNA binding motif protein 28 23029 RBM34 RNA binding motif protein 34 57109 REXO4 REX4 homolog, 3'-5' exonuclease 83732 RIOK1 RIO kinase 1 55781 RIOK2 RIO kinase 2 8780 RIOK3 RIO kinase 3 4734 RPF1 neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase 23076 RRP1 ribosomal RNA processing 1B 51018 RRP15 ribosomal RNA processing 15 homolog 23076 RRP1B ribosomal RNA processing 1B 88745 RRP36 ribosomal RNA processing 36 23378 RRP8 ribosomal RNA processing 8 303076 SURF6 surfeit 6 93587 TRMT10A tRNA methyltransferase 10A 158234 TRMT10B tRNA methyltransferase 10B 54931 TRMT10C tRNA methyltransferase 10C, mitochondrial RNase P subunit 115708 TRMT61A tRNA methyltransferase 61A 55006 TRMT61B tRNA methyltransferase 61B 90121 TSR2 TSR2, ribosome maturation factor 51118 UTP11L UTP11, small subunit processome component 84294 UTP23 UTP23, small subunit processome component 57050 UTP3 UTP3, small subunit processome component 114049 WBSCR22 BUD23, rRNA methyltransferase and ribosome maturation factor 155368 WBSCR27 methyltransferase like 27 54663 WDR74 WD repeat domain 74 54680 ZNHIT6 zinc finger HIT-type containing 6

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 4.19e-01 6.19e-17 GO preribosome, small subunit precursor cellular_component 2.13e-01 1.97e-18 GO preribosome, large subunit precursor cellular_component 7.30e-02 3.64e-06 GO mRNA methylation biological_process 6.00e-02 5.93e-10 GO ribosomal small subunit biogenesis biological_process 5.52e-02 1.33e-08 GO tRNA methylation biological_process 4.23e-02 4.73e-25 GO rRNA processing biological_process 5.73e-03 2.39e-04 Reactome tRNA modification in the mitochondrion Metabolism of RNA 5.64e-04 2.04e-10 Reactome rRNA modification in the nucleus and cytosol Metabolism of RNA 2.84e-04 2.00e-08 GO maturation of SSU-rRNA 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 0.00e+00 0.00e+00 ribosome biogenesis 0.00e+00 0.00e+00 ribonucleoprotein complex biogenesis 0.00e+00 0.00e+00 maturation of SSU-rRNA 0.00e+00 0.00e+00 rRNA processing 0.00e+00 0.00e+00 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) 0.00e+00 0.00e+00 rRNA metabolic process 0.00e+00 0.00e+00 ribosomal small subunit biogenesis 0.00e+00 0.00e+00 ribosomal large subunit biogenesis 0.00e+00 0.00e+00 intracellular ribonucleoprotein complex 0.00e+00 0.00e+00 ribonucleoprotein complex 0.00e+00 0.00e+00 preribosome, large subunit precursor 2.43e-11 2.14e-08 cleavage involved in rRNA processing 3.89e-11 2.45e-08 rRNA binding 1.21e-10 6.17e-08 preribosome, small subunit precursor 5.68e-10 4.36e-07 maturation of 5.8S rRNA 3.51e-09 2.43e-06 ribosome assembly 9.75e-09 4.46e-06 tRNA (adenine-N1-)-methyltransferase activity 1.82e-08 1.14e-05 ribosomal large subunit assembly 2.50e-08 1.55e-05 nucleic acid phosphodiester bond hydrolysis 5.14e-08 3.04e-05 endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.65e-03 1.81e-01 NRAGE SIGNALS DEATH THROUGH JNK 3.31e-03 3.26e-01 CELL DEATH SIGNALLING VIA NRAGE NRIF AND NADE 7.35e-03 6.25e-01 P75 NTR RECEPTOR MEDIATED SIGNALLING 8.29e-03 6.90e-01 SIGNALLING BY NGF

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.87e-03 1e+00 skin hyperplasia 1.88e-03 1e+00 increased histiocytic sarcoma incidence 3.44e-03 1e+00 increased circulating magnesium level 3.74e-03 1e+00 failure of morula compaction 3.74e-03 1e+00 failure of blastocyst formation 5.61e-03 1e+00 abnormal primordial germ cell proliferation 7.18e-03 1e+00 increased mammary gland tumor incidence 7.47e-03 1e+00 increased gastrointestinal tumor incidence 7.48e-03 1e+00 decreased primordial germ cell number 7.49e-03 1e+00 increased lung tumor incidence 9.03e-03 1e+00 abnormal telomere length 9.04e-03 1e+00 abnormal preimplantation embryo development 9.34e-03 1e+00 increased liver tumor incidence 9.34e-03 1e+00 increased hemangiosarcoma incidence 9.34e-03 1e+00 absent heartbeat 1.12e-02 1e+00 failure to form blastocele 1.31e-02 1e+00 increased carcinoma incidence 2.78e-02 1e+00 increased sarcoma incidence 2.92e-02 1e+00 abnormal cell morphology 3.19e-02 1e+00 pallor

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

²FDR corrected p-value (Benjamini-Hochberg)