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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod345

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod345 Module size 58 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 161823 ADAL adenosine deaminase like 91801 ALKBH8 alkB homolog 8, tRNA methyltransferase 60314 C12orf10 chromosome 12 open reading frame 10 65265 C8orf33 chromosome 8 open reading frame 33 138241 C9orf85 chromosome 9 open reading frame 85 79080 CCDC86 coiled-coil domain containing 86 348180 CTU2 cytosolic thiouridylase subunit 2 83475 DOHH deoxyhypusine hydroxylase 51611 DPH5 diphthamide biosynthesis 5 51534 DRG1 vesicle trafficking 1 1819 DRG2 developmentally regulated GTP binding protein 2 56931 DUS3L dihydrouridine synthase 3 like 11062 DUS4L dihydrouridine synthase 4 like 3692 EIF6 eukaryotic translation initiation factor 6 84908 FAM136A family with sequence similarity 136 member A 65990 FAM173A family with sequence similarity 173 member A 1258 GAR1 cyclic nucleotide gated channel beta 1 51184 GPN3 GPN-loop GTPase 3 55272 IMP3 IMP3, U3 small nucleolar ribonucleoprotein 57604 KIAA1456 tRNA methyltransferase 9B (putative) 84298 LLPH LLP homolog, long-term synaptic facilitation factor 4234 METTL1 methyltransferase like 1 399818 METTL10 EEF1A lysine methyltransferase 2 151194 METTL21A methyltransferase like 21A 196541 METTL21C methyltransferase like 21C 51154 MRTO4 MRT4 homolog, ribosome maturation factor 92170 MTG1 mitochondrial ribosome associated GTPase 1 55651 NHP2 NHP2 ribonucleoprotein 84273 NOA1 nitric oxide associated 1 51406 NOL7 nucleolar protein 7 55035 NOL8 nucleolar protein 8 55505 NOP10 NOP10 ribonucleoprotein 51491 NOP16 NOP16 nucleolar protein 10412 NSA2 NSA2, ribosome biogenesis homolog 55239 OGFOD1 2-oxoglutarate and iron dependent oxygenase domain containing 1 84172 POLR1B RNA polymerase I subunit B 64425 POLR1E RNA polymerase I subunit E 23082 PPRC1 peroxisome proliferator-activated receptor gamma, coactivator-related 1 57455 REXO1 RNA exonuclease 1 homolog 254958 REXO1L1 REXO1 like 1, pseudogene NA REXO1L10P 22934 RPIA ribose 5-phosphate isomerase A 10557 RPP38 ribonuclease P/MRP subunit p38 51187 RSL24D1 ribosomal L24 domain containing 1 51389 RWDD1 RWD domain containing 1 201965 RWDD4 RWD domain containing 4 297483 SHQ1 SHQ1, H/ACA ribonucleoprotein assembly factor 84068 SLC10A7 solute carrier family 10 member 7 402055 SRRD SRR1 domain containing 100361518 SSB - 55319 TMA16 translation machinery associated 16 homolog 51504 TRMT112 tRNA methyltransferase subunit 11-2 221830 TWISTNB TWIST neighbor 10785 WDR4 WD repeat domain 4 54853 WDR55 WD repeat domain 55 112840 WDR89 WD repeat domain 89 55854 ZC3H15 zinc finger CCCH-type containing 15 51042 ZNF593 zinc finger protein 593

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 1.78e-01 1.79e-07 GO box H/ACA snoRNP complex cellular_component 1.73e-01 1.79e-07 GO box H/ACA snoRNA binding molecular_function 8.89e-02 3.89e-06 GO RNA polymerase I activity molecular_function 3.32e-02 8.70e-08 Reactome tRNA modification in the nucleus and cytosol Metabolism of RNA 2.57e-02 3.11e-04 GO protein methyltransferase activity molecular_function 1.77e-02 3.07e-05 GO preribosome, large subunit precursor cellular_component 8.85e-03 4.55e-04 GO peptidyl-lysine methylation biological_process 2.62e-03 5.37e-04 GO ribosomal large subunit binding molecular_function 1.67e-03 5.05e-06 GO RNA polymerase I complex cellular_component

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 metabolic process 0.00e+00 0.00e+00 ribosome biogenesis 0.00e+00 0.00e+00 ribonucleoprotein complex biogenesis 0.00e+00 0.00e+00 RNA modification 0.00e+00 0.00e+00 tRNA modification 0.00e+00 0.00e+00 intracellular ribonucleoprotein complex 0.00e+00 0.00e+00 ribonucleoprotein complex 7.04e-11 5.94e-08 tRNA processing 1.07e-10 8.85e-08 rRNA processing 7.83e-10 5.91e-07 ribosomal large subunit biogenesis 2.08e-09 1.05e-06 methyltransferase activity 3.77e-09 2.59e-06 tRNA metabolic process 7.27e-08 2.54e-05 box H/ACA telomerase RNP complex 7.27e-08 2.54e-05 box H/ACA scaRNP complex 7.64e-08 4.40e-05 methylation 2.19e-07 1.17e-04 rRNA pseudouridine synthesis 2.20e-07 7.05e-05 box H/ACA snoRNP complex 4.17e-07 1.42e-04 box H/ACA snoRNA binding 6.20e-07 2.04e-04 tRNA binding 7.31e-07 3.57e-04 RNA (guanine-N7)-methylation

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.40e-03 2.18e-01 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 2.84e-03 2.53e-01 TRANSCRIPTION 3.84e-03 3.67e-01 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 6.45e-03 5.11e-01 RNA POL III TRANSCRIPTION TERMINATION 7.41e-03 5.73e-01 EXTENSION OF TELOMERES 1.08e-02 8.46e-01 RNA POL I TRANSCRIPTION TERMINATION 1.14e-02 8.84e-01 TRANSCRIPTION 1.15e-02 8.90e-01 ABACAVIR TRANSPORT AND METABOLISM 1.16e-02 8.96e-01 EXTENSION OF TELOMERES 1.17e-02 9.02e-01 RNA POL I TRANSCRIPTION INITIATION 1.34e-02 1.00e+00 TELOMERE MAINTENANCE 1.40e-02 9.61e-01 RNA POL I TRANSCRIPTION TERMINATION 1.52e-02 1.00e+00 RNA POL III TRANSCRIPTION TERMINATION 1.64e-02 1.00e+00 PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION 1.72e-02 1.00e+00 RNA POL I TRANSCRIPTION INITIATION 1.79e-02 1.00e+00 PURINE SALVAGE 2.01e-02 1.00e+00 TELOMERE MAINTENANCE 2.04e-02 1.00e+00 ABACAVIR TRANSPORT AND METABOLISM 2.33e-02 1.00e+00 PURINE SALVAGE 2.46e-02 1.00e+00 RNA POL I TRANSCRIPTION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.55e-03 1e+00 inner cell mass degeneration 5.62e-03 1e+00 abnormal corticosterone level 9.35e-03 1e+00 abnormal mitochondrial crista morphology 9.37e-03 1e+00 abnormal fat cell morphology 1.12e-02 1e+00 abnormal nucleolus morphology 1.12e-02 1e+00 embryo tissue necrosis 1.15e-02 1e+00 abnormal spleen morphology 1.30e-02 1e+00 increased fasted circulating glucose level 1.30e-02 1e+00 delayed blastocyst hatching from the zona pellucida 1.31e-02 1e+00 abnormal hepatocyte physiology 1.61e-02 1e+00 complete preweaning lethality 1.86e-02 1e+00 abnormal T cell morphology 1.87e-02 1e+00 liver hypoplasia 2.05e-02 1e+00 disorganized embryonic tissue 2.05e-02 1e+00 decreased apoptosis 2.23e-02 1e+00 preweaning lethality 2.23e-02 1e+00 decreased T cell apoptosis 2.37e-02 1e+00 embryonic lethality prior to organogenesis 2.55e-02 1e+00 abnormal mitochondrial ATP synthesis coupled electron transport 2.78e-02 1e+00 abnormal trophoblast giant cells

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

²FDR corrected p-value (Benjamini-Hochberg)