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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod291

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod291 Module size 41 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 23468 CBX5 chromobox 5 8099 CDK2AP1 cyclin dependent kinase 2 associated protein 1 1107 CHD3 chromodomain helicase DNA binding protein 3 1108 CHD4 chromodomain helicase DNA binding protein 4 1786 DNMT1 DNA methyltransferase 1 1788 DNMT3A DNA methyltransferase 3 alpha 1789 DNMT3B DNA methyltransferase 3 beta 58516 FAM60A SIN3-HDAC complex associated factor 54815 GATAD2A GATA zinc finger domain containing 2A 54556 ING2 inhibitor of growth family member 3 338645 LUZP2 leucine zipper protein 2 8932 MBD2 methyl-CpG binding domain protein 2 53615 MBD3 methyl-CpG binding domain protein 3 85509 MBD3L1 methyl-CpG binding domain protein 3 like 1 125997 MBD3L2 methyl-CpG binding domain protein 3 like 2 9112 MTA1 metastasis associated 1 9219 MTA2 metastasis associated 1 family member 2 57504 MTA3 metastasis associated 1 family member 3 57649 PHF12 PHD finger protein 12 51317 PHF21A PHD finger protein 21A 5928 RBBP4 RB binding protein 4, chromatin remodeling factor 5931 RBBP7 RB binding protein 7, chromatin remodeling factor 473 RERE arginine-glutamic acid dipeptide repeats 304714 RRN3 RRN3 homolog, RNA polymerase I transcription factor 6299 SALL1 spalt like transcription factor 1 6297 SALL2 spalt like transcription factor 2 290284 SAP18 Sin3A associated protein 18 8819 SAP30 Sin3A associated protein 30 29115 SAP30BP SAP30 binding protein 79685 SAP30L SAP30 like 23314 SATB2 SATB homeobox 2 23544 SEZ6L seizure related 6 homolog like 64426 SUDS3 SDS3 homolog, SIN3A corepressor complex component 9015 TAF1A TATA-box binding protein associated factor, RNA polymerase I subunit A 9014 TAF1B TATA-box binding protein associated factor, RNA polymerase I subunit B 9013 TAF1C TATA-box binding protein associated factor, RNA polymerase I subunit C 79101 TAF1D TATA-box binding protein associated factor, RNA polymerase I subunit D 6913 TBX15 T-box 15 7270 TTF1 transcription termination factor 1 7343 UBTF upstream binding transcription factor 84619 ZGPAT zinc finger CCCH-type and G-patch domain containing

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 3.22e-01 5.51e-26 GO NuRD complex cellular_component 2.50e-01 1.58e-09 GO RNA polymerase I CORE element sequence-specific DNA binding molecular_function 1.28e-01 1.52e-28 GO histone deacetylase activity molecular_function 1.10e-01 5.87e-11 GO methylation-dependent chromatin silencing biological_process 1.01e-01 5.34e-17 GO histone deacetylase complex cellular_component 7.76e-02 2.34e-43 Reactome Epigenetic regulation of gene expression Gene expression (Transcription) 2.84e-02 5.94e-06 Reactome SUMOylation of DNA methylation proteins Metabolism of proteins 1.82e-02 1.51e-09 GO DNA methylation biological_process 1.51e-02 2.94e-09 GO methyl-CpG binding molecular_function 6.02e-03 1.73e-12 Reactome RNA Polymerase I Transcription Gene expression (Transcription) 3.47e-03 6.80e-03 Reactome Defective pro-SFTPB causes pulmonary surfactant metabolism dysfunction 1 (SMDP1) and respiratory distress syndrome (RDS) Disease

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 negative regulation of transcription from RNA polymerase II promoter 0.00e+00 0.00e+00 covalent chromatin modification 0.00e+00 0.00e+00 negative regulation of gene expression, epigenetic 0.00e+00 0.00e+00 chromatin organization 0.00e+00 0.00e+00 regulation of gene expression, epigenetic 0.00e+00 0.00e+00 protein deacetylation 0.00e+00 0.00e+00 histone modification 0.00e+00 0.00e+00 histone deacetylation 0.00e+00 0.00e+00 transcriptional repressor complex 0.00e+00 0.00e+00 NuRD complex 0.00e+00 0.00e+00 histone deacetylase complex 0.00e+00 0.00e+00 SWI/SNF superfamily-type complex 0.00e+00 0.00e+00 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0.00e+00 0.00e+00 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides 0.00e+00 0.00e+00 histone deacetylase activity 0.00e+00 0.00e+00 chromatin binding 0.00e+00 0.00e+00 deacetylase activity 0.00e+00 0.00e+00 protein deacetylase activity 2.25e-11 1.98e-08 transcription initiation from RNA polymerase I promoter 2.96e-11 2.58e-08 chromatin remodeling

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 5.56e-12 1.64e-09 RNA POL I TRANSCRIPTION 3.23e-10 1.12e-07 RNA POL I TRANSCRIPTION INITIATION 5.52e-10 1.39e-07 RNA POL I TRANSCRIPTION INITIATION 1.01e-09 2.46e-07 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 1.88e-09 5.98e-07 RNA POL I TRANSCRIPTION 2.75e-09 6.38e-07 TRANSCRIPTION 2.47e-08 6.91e-06 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 3.04e-08 8.41e-06 RNA POL I TRANSCRIPTION TERMINATION 7.39e-08 1.46e-05 RNA POL I TRANSCRIPTION TERMINATION 2.19e-07 5.45e-05 TRANSCRIPTION 6.47e-05 8.52e-03 RNA POL I PROMOTER OPENING 3.05e-03 3.05e-01 RNA POL I PROMOTER OPENING 3.65e-03 3.14e-01 DEPOSITION OF NEW CENPA CONTAINING NUCLEOSOMES AT THE CENTROMERE 5.45e-03 4.91e-01 DEPOSITION OF NEW CENPA CONTAINING NUCLEOSOMES AT THE CENTROMERE 1.31e-02 9.12e-01 CHROMOSOME MAINTENANCE 1.52e-02 1.00e+00 CHROMOSOME MAINTENANCE 3.17e-02 1.00e+00 G0 AND EARLY G1 3.43e-02 1.00e+00 G0 AND EARLY G1

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.89e-04 5.99e-01 open neural tube 7.55e-04 7.64e-01 abnormal DNA methylation 1.18e-03 9.89e-01 incomplete rostral neuropore closure 1.49e-03 1.00e+00 abnormal temporal bone morphology 1.80e-03 1.00e+00 ocular hypertelorism 2.54e-03 1.00e+00 increased sacral vertebrae number 2.60e-03 1.00e+00 abnormal nasal bone morphology 3.11e-03 1.00e+00 short snout 3.72e-03 1.00e+00 single kidney 5.00e-03 1.00e+00 lumbar vertebral transformation 5.77e-03 1.00e+00 decreased lumbar vertebrae number 6.10e-03 1.00e+00 abnormal embryo turning 6.26e-03 1.00e+00 abnormal snout morphology 6.87e-03 1.00e+00 absent kidney 7.50e-03 1.00e+00 wide frontal bone 7.52e-03 1.00e+00 abnormal scapular spine morphology 8.54e-03 1.00e+00 abnormal thoracic vertebrae morphology 9.36e-03 1.00e+00 abnormal hyoid bone body morphology 9.94e-03 1.00e+00 abnormal mandible morphology 1.12e-02 1.00e+00 microstomia

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

²FDR corrected p-value (Benjamini-Hochberg)