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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod51

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod51 Module size 100 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 6059 ABCE1 ATP binding cassette subfamily E member 1 23 ABCF1 ATP binding cassette subfamily F member 1 10061 ABCF2 ATP binding cassette subfamily F member 2 55324 ABCF3 ATP binding cassette subfamily F member 3 340351 AGBL3 ATP/GTP binding protein like 3 54784 ALKBH4 alkB homolog 4, lysine demethylase 341405 ANKRD33 ankyrin repeat domain 33 317 APAF1 apoptotic peptidase activating factor 1 362170 API5 apoptosis inhibitor 5 110599588 ASNSD1 ASNSD1 upstream reading frame 55210 ATAD3A ATPase family, AAA domain containing 3A 219293 ATAD3C ATPase family, AAA domain containing 3C 283643 C14orf80 tubulin epsilon and delta complex 1 63920 C5orf54 zinc finger BED-type containing 8 10849 CD3EAP CD3e molecule associated protein 54901 CDKAL1 CDK5 regulatory subunit associated protein 1 like 1 90353 CTU1 cytosolic thiouridylase subunit 1 51260 CXorf26 polysaccharide biosynthesis domain containing 1 681234 DBR1 debranching RNA lariats 1 1725 DHPS deoxyhypusine synthase 1735 DIO3 iodothyronine deiodinase 3 25312 DMP1 dentin matrix acidic phosphoprotein 1 134218 DNAJC21 DnaJ heat shock protein family (Hsp40) member C21 1801 DPH1 diphthamide biosynthesis 1 1802 DPH2 DPH2 homolog 29102 DROSHA drosha ribonuclease III 54920 DUS2L dihydrouridine synthase 2 55140 ELP3 elongator acetyltransferase complex subunit 3 2021 ENDOG endonuclease G 9941 EXOG exo/endonuclease G 54942 FAM206A family with sequence similarity 206 member A 85395 FAM207A family with sequence similarity 207 member A 85002 FAM86B1 family with sequence similarity 86 member B1 55199 FAM86C1 family with sequence similarity 86 member C1 8833 GMPS guanine monophosphate synthase 11321 GPN1 GPN-loop GTPase 1 3475 IFRD1 interferon related developmental regulator 1 7866 IFRD2 interferon related developmental regulator 2 3669 ISG20 interferon stimulated exonuclease gene 20 9692 KIAA0391 KIAA0391 81887 LAS1L LAS1 like, ribosome biogenesis factor 84247 LDOC1L retrotransposon Gag like 6 79727 LIN28A lin-28 homolog A 339175 METTL2A methyltransferase like 2A 29081 METTL5 methyltransferase like 5 79828 METTL8 methyltransferase like 8 84864 MINA ribosomal oxygenase 2 4494 MT1F metallothionein 1F 130916 MTERFD2 mitochondrial transcription termination factor 4 84939 MUM1 melanoma associated antigen (mutated) 1 79133 NDUFAF5 NADH:ubiquinone oxidoreductase complex assembly factor 5 9147 NEMF nuclear export mediator factor 79707 NOL9 nucleolar protein 9 9315 NREP neuronal regeneration related protein 54888 NSUN2 NOP2/Sun RNA methyltransferase family member 2 63899 NSUN3 NOP2/Sun RNA methyltransferase family member 3 387338 NSUN4 NOP2/Sun RNA methyltransferase family member 4 55695 NSUN5 NOP2/Sun RNA methyltransferase family member 5 79730 NSUN7 NOP2/Sun RNA methyltransferase family member 7 91181 NUP210L nucleoporin 210 like 124641 OVCA2 OVCA2, serine hydrolase domain containing 728361 OVOL3 ovo like zinc finger 3 63935 PCIF1 PDX1 C-terminal inhibiting factor 1 80235 PIGZ phosphatidylinositol glycan anchor biosynthesis class Z 120379 PIH1D2 PIH1 domain containing 2 25885 POLR1A RNA polymerase I subunit A 5442 POLRMT RNA polymerase mitochondrial 26472 PPP1R14B protein phosphatase 1 regulatory inhibitor subunit 14B 9858 PPP1R26 protein phosphatase 1 regulatory subunit 26 100911617 PRMT5 protein arginine N-methyltransferase 6-like 54496 PRMT7 protein arginine methyltransferase 7 80324 PUS1 pseudouridylate synthase 1 150962 PUS10 pseudouridylate synthase 10 NA REXO1L11P 25996 REXO2 RNA exonuclease 2 727800 RNF208 ring finger protein 208 6101 RP1 RP1, axonemal microtubule associated 222194 RSBN1L round spermatid basic protein 1 like 79918 SETD6 SET domain containing 6 256536 TCERG1L transcription elongation regulator 1 like 63892 THADA THADA, armadillo repeat containing 80745 THUMPD2 THUMP domain containing 2 25917 THUMPD3 THUMP domain containing 3 55039 TRMT12 tRNA methyltransferase 12 homolog 54482 TRMT13 tRNA methyltransferase 13 homolog 152992 TRMT44 tRNA methyltransferase 44 homolog 57570 TRMT5 tRNA methyltransferase 5 51095 TRNT1 tRNA nucleotidyl transferase 1 26995 TRUB2 TruB pseudouridine synthase family member 2 7247 TSN translin 115939 TSR3 TSR3, acp transferase ribosome maturation factor 7268 TTC4 tetratricopeptide repeat domain 4 55253 TYW1 tRNA-yW synthesizing protein 1 homolog 499731 TYW3 tRNA-yW synthesizing protein 3 homolog 222008 VSTM2A V-set and transmembrane domain containing 2A 84219 WDR24 WD repeat domain 24 55135 WRAP53 WD repeat containing antisense to TP53 11260 XPOT exportin for tRNA 56829 ZC3HAV1 zinc finger CCCH-type containing, antiviral 1 8882 ZNF259 ZPR1 zinc finger

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 3.03e-01 8.31e-09 Reactome Synthesis of wybutosine at G37 of tRNA(Phe) Metabolism of RNA 1.72e-01 1.41e-16 GO tRNA methylation biological_process 1.17e-01 1.37e-05 GO pseudouridine synthase activity molecular_function 1.07e-01 2.24e-15 GO methyltransferase activity molecular_function 8.02e-02 5.00e-04 GO maturation of 5.8S rRNA biological_process 7.70e-02 5.00e-04 Reactome Synthesis of diphthamide-EEF2 Metabolism of proteins 2.78e-02 1.06e-03 GO retinal cone cell development biological_process 2.69e-02 1.48e-02 GO dihydrofolate reductase activity molecular_function 2.69e-02 1.48e-02 Reactome Formation of apoptosome Programmed Cell Death 2.69e-02 1.48e-02 Reactome Mitochondrial transcription initiation Gene expression (Transcription) 2.56e-02 6.60e-15 Reactome tRNA modification in the nucleus and cytosol Metabolism of RNA 1.96e-02 1.29e-03 GO DNA catabolic process, endonucleolytic biological_process 1.81e-02 1.48e-02 Reactome Regulation of thyroid hormone activity Metabolism 5.91e-03 8.52e-04 GO histone-arginine N-methyltransferase activity molecular_function 3.97e-03 6.65e-04 GO peptidyl-diphthamide biosynthetic process from peptidyl-histidine biological_process 2.91e-03 8.52e-04 GO histone arginine methylation biological_process 1.01e-03 2.40e-04 GO tRNA (cytosine-5-)-methyltransferase activity molecular_function 6.48e-04 1.77e-08 GO tRNA 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 tRNA modification 0.00e+00 0.00e+00 methyltransferase activity 3.20e-18 3.05e-15 tRNA processing 1.80e-16 1.70e-13 methylation 3.23e-15 3.04e-12 tRNA metabolic process 3.69e-15 3.47e-12 RNA modification 1.53e-10 9.15e-08 RNA methyltransferase activity 2.48e-10 1.98e-07 RNA methylation 3.56e-09 2.46e-06 tRNA methylation 4.49e-09 2.15e-06 S-adenosylmethionine-dependent methyltransferase activity 4.65e-09 2.22e-06 tRNA methyltransferase activity 5.77e-07 2.87e-04 mitochondrial tRNA processing 7.48e-07 3.64e-04 ribonucleoprotein complex biogenesis 1.05e-06 3.31e-04 nuclease activity 1.18e-06 5.53e-04 mitochondrial RNA processing 2.18e-06 9.70e-04 ribosome biogenesis 4.67e-06 1.94e-03 rRNA modification 5.81e-06 1.59e-03 tRNA binding 6.64e-06 1.68e-03 mitochondrial matrix 6.65e-06 2.67e-03 rRNA metabolic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 5.76e-04 6.14e-02 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 7.91e-04 8.14e-02 TRANSCRIPTION 7.06e-03 6.05e-01 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 1.08e-02 7.78e-01 RNA POL I TRANSCRIPTION INITIATION 1.08e-02 7.78e-01 RNA POL I TRANSCRIPTION TERMINATION 1.25e-02 8.83e-01 EXTENSION OF TELOMERES 1.35e-02 9.36e-01 RNA POL I TRANSCRIPTION 2.00e-02 1.00e+00 TRANSCRIPTION 2.50e-02 1.00e+00 AMINE DERIVED HORMONES 2.52e-02 1.00e+00 TELOMERE MAINTENANCE 2.72e-02 1.00e+00 PURINE RIBONUCLEOSIDE MONOPHOSPHATE BIOSYNTHESIS 3.07e-02 1.00e+00 PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION 3.16e-02 1.00e+00 PURINE RIBONUCLEOSIDE MONOPHOSPHATE BIOSYNTHESIS 3.30e-02 1.00e+00 RNA POL I TRANSCRIPTION TERMINATION 3.35e-02 1.00e+00 INTERFERON ALPHA BETA SIGNALING 3.45e-02 1.00e+00 REGULATORY RNA PATHWAYS 3.45e-02 1.00e+00 MICRORNA MIRNA BIOGENESIS 3.83e-02 1.00e+00 RNA POL I TRANSCRIPTION INITIATION 4.27e-02 1.00e+00 EXTENSION OF TELOMERES 4.44e-02 1.00e+00 INTRINSIC PATHWAY FOR APOPTOSIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.67e-03 1e+00 abnormal sperm midpiece morphology 2.90e-03 1e+00 preweaning lethality 4.53e-03 1e+00 abnormal retinal neuronal layer morphology 5.18e-03 1e+00 decreased sensitivity to induced cell death 6.55e-03 1e+00 abnormal craniofacial bone morphology 7.50e-03 1e+00 midbrain hyperplasia 7.50e-03 1e+00 flat head 7.72e-03 1e+00 decreased fetal weight 9.35e-03 1e+00 persistence of medial edge epithelium during palatal shelf fusion 1.12e-02 1e+00 abnormal pituitary hormone level 1.12e-02 1e+00 abnormal thyroid hormone level 1.12e-02 1e+00 abnormal circulating interleukin-4 level 1.12e-02 1e+00 absent palatine bone 1.12e-02 1e+00 abnormal folding of telencephalic vesicles 1.12e-02 1e+00 absent neurocranium 1.31e-02 1e+00 increased alkaline phosphatase activity 1.46e-02 1e+00 decreased body length 1.49e-02 1e+00 abnormal hair shedding 1.49e-02 1e+00 increased triiodothyronine level 1.49e-02 1e+00 abnormal pulp cavity morphology

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

²FDR corrected p-value (Benjamini-Hochberg)