Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod330

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod330 Module size 86 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name NA AGAP10 9790 BMS1 BMS1, ribosome biogenesis factor 705 BYSL bystin like 1649 CEBPZ DNA damage inducible transcript 3 283489 CHAMP1 chromosome alignment maintaining phosphoprotein 1 84916 CIRH1A UTP4, small subunit processome component 25879 DCAF13 DDB1 and CUL4 associated factor 13 57062 DDX24 DEAD-box helicase 24 55661 DDX27 DEAD-box helicase 27 158067 DDX31 adenylate kinase 8 317781 DDX51 DEAD-box helicase 51 11056 DDX52 DExD-box helicase 52 79039 DDX54 DEAD-box helicase 54 57696 DDX55 DEAD-box helicase 55 54606 DDX56 DEAD-box helicase 56 91351 DDX60L DExD/H-box 60 like 57647 DHX37 DEAH-box helicase 37 27042 DIEXF UTP25, small subunit processor component 55520 ELAC1 elaC ribonuclease Z 1 24140 FTSJ1 FtsJ RNA methyltransferase homolog 1 29960 FTSJ2 mitochondrial rRNA methyltransferase 2 117246 FTSJ3 FtsJ RNA methyltransferase homolog 3 2593 GAMT guanidinoacetate N-methyltransferase 2794 GNL1 G protein nucleolar 1 (putative) 29889 GNL2 G protein nucleolar 2 26354 GNL3 G protein nucleolar 3 344758 GPR149 G protein-coupled receptor 149 23560 GTPBP4 GTP binding protein 4 55127 HEATR1 HEAT repeat containing 1 9933 KIAA0020 pumilio RNA binding family member 3 100505753 KRTAP16-1 keratin associated protein 16-1 55341 LSG1 large 60S subunit nuclear export GTPase 1 10199 MPHOSPH10 M-phase phosphoprotein 10 10514 MYBBP1A MYB binding protein 1a 55226 NAT10 N-acetyltransferase 10 54475 NLE1 notchless homolog 1 26155 NOC2L NOC2 like nucleolar associated transcriptional repressor 64318 NOC3L NOC3 like DNA replication regulator 79050 NOC4L nucleolar complex associated 4 homolog 79954 NOL10 nucleolar protein 10 25926 NOL11 nucleolar protein 11 65083 NOL6 nucleolar protein 6 64434 NOM1 nucleolar protein with MIF4G domain 1 8602 NOP14 NOP14 nucleolar protein 161424 NOP9 NOP9 nucleolar protein 221078 NSUN6 NOP2/Sun RNA methyltransferase family member 6 4931 NVL nuclear VCP-like 55003 PAK1IP1 PAK1 interacting protein 1 22984 PDCD11 programmed cell death 11 23481 PES1 pescadillo ribosomal biogenesis factor 1 26121 PRPF31 pre-mRNA processing factor 31 54517 PUS7 pseudouridylate synthase 7 83448 PUS7L pseudouridylate synthase 7 like 11137 PWP1 PWP1 homolog, endonuclein 5822 PWP2 PWP2, small subunit processome component 9904 RBM19 RNA binding motif protein 19 10171 RCL1 RNA terminal phosphate cyclase like 1 84154 RPF2 ribosome production factor 2 homolog 23223 RRP12 ribosomal RNA processing 12 homolog 27341 RRP7A ribosomal RNA processing 7 homolog A 9136 RRP9 ribosomal RNA processing 9, U3 small nucleolar RNA binding protein 26156 RSL1D1 ribosomal L1 domain containing 1 8634 RTCA RNA 3'-terminal phosphate cyclase 55153 SDAD1 SDA1 domain containing 1 10607 TBL3 transducin beta like 3 91646 TDRD12 tudor domain containing 12 56157 TEX13A testis expressed 13A 60487 TRMT11 tRNA methyltransferase 11 homolog 81627 TRMT1L tRNA methyltransferase 1 like 27037 TRMT2A tRNA methyltransferase 2 homolog A 79979 TRMT2B tRNA methyltransferase 2 homolog B 51605 TRMT6 tRNA methyltransferase 6 55720 TSR1 TSR1, ribosome maturation factor 55622 TTC27 tetratricopeptide repeat domain 27 10813 UTP14A UTP14A, small subunit processome component 9724 UTP14C UTP14C, small subunit processome component 84135 UTP15 UTP15, small subunit processome component 51096 UTP18 UTP18, small subunit processome component 27340 UTP20 UTP20, small subunit processome component 55813 UTP6 UTP6, small subunit processome component 10885 WDR3 WD repeat domain 3 134430 WDR36 WD repeat domain 36 23160 WDR43 WD repeat domain 43 9277 WDR46 WD repeat domain 46 11180 WDR6 WD repeat domain 6 84128 WDR75 WD repeat domain 75

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 2.54e-01 5.34e-55 Reactome rRNA modification in the nucleus and cytosol Metabolism of RNA 2.11e-01 3.72e-08 GO maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) biological_process 1.45e-01 4.75e-25 GO maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) biological_process 1.31e-01 6.74e-39 GO small-subunit processome cellular_component 6.63e-02 1.67e-09 GO ribosomal large subunit biogenesis biological_process 5.55e-02 1.45e-07 GO positive regulation of transcription by RNA polymerase I biological_process 5.29e-02 1.58e-07 GO tRNA methylation biological_process 4.25e-02 8.65e-06 GO preribosome, small subunit precursor cellular_component 3.61e-02 1.50e-10 GO 90S preribosome cellular_component 3.35e-02 2.60e-49 GO rRNA processing biological_process 8.43e-03 9.08e-07 Reactome tRNA modification in the nucleus and cytosol Metabolism of RNA 1.64e-03 7.84e-04 GO pseudouridine synthase activity molecular_function 8.66e-04 7.84e-04 GO positive regulation of transcription of nucleolar large rRNA by RNA polymerase I 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 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 maturation of SSU-rRNA 0.00e+00 0.00e+00 ribosomal small subunit biogenesis 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 small-subunit processome 0.00e+00 0.00e+00 intracellular ribonucleoprotein complex 0.00e+00 0.00e+00 Pwp2p-containing subcomplex of 90S preribosome 0.00e+00 0.00e+00 ribonucleoprotein complex 0.00e+00 0.00e+00 90S preribosome 0.00e+00 0.00e+00 snoRNA binding 1.20e-10 9.88e-08 RNA secondary structure unwinding 1.62e-10 1.32e-07 RNA modification 3.87e-10 2.20e-07 RNA methyltransferase activity 1.11e-09 5.85e-07 U3 snoRNA binding 1.22e-09 8.98e-07 RNA methylation 1.47e-09 7.60e-07 helicase activity 5.35e-09 3.60e-06 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)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.40e-05 8.81e-02 failure to form blastocele 8.57e-04 8.25e-01 embryonic growth arrest 1.18e-03 9.89e-01 complete embryonic lethality before implantation 1.32e-03 1.00e+00 complete preweaning lethality 2.86e-03 1.00e+00 abnormal preimplantation embryo development 3.74e-03 1.00e+00 increased mature ovarian follicle number 3.75e-03 1.00e+00 facial cleft 3.75e-03 1.00e+00 decreased hindbrain size 3.75e-03 1.00e+00 prolonged estrus 5.47e-03 1.00e+00 complete embryonic lethality 5.62e-03 1.00e+00 failure of blastocyst to hatch from the zona pellucida 7.48e-03 1.00e+00 abnormal circulating creatinine level 7.48e-03 1.00e+00 limp posture 7.49e-03 1.00e+00 abnormal nasal septum morphology 7.50e-03 1.00e+00 abnormal estrous cycle 1.12e-02 1.00e+00 increased midbrain size 1.12e-02 1.00e+00 abnormal brain ventricle morphology 1.12e-02 1.00e+00 abnormal urine amino acid level 1.12e-02 1.00e+00 increased litter size 1.30e-02 1.00e+00 failure of neuromuscular synapse postsynaptic differentiation

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

²FDR corrected p-value (Benjamini-Hochberg)