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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod77

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod77 Module size 38 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 474382 H2AFB1 H2A histone family member B1 474381 H2AFB2 H2A histone family member B2 83740 H2AFB3 H2A histone family member B3 55766 H2AFJ H2A histone family member J 9555 H2AFY H2A histone family member Y 55506 H2AFY2 H2A histone family member Y2 286436 H2BFM H2B histone family member M 221613 HIST1H2AA histone cluster 1 H2A family member a 8335 HIST1H2AB histone cluster 1 H2A family member b 8334 HIST1H2AC histone cluster 1 H2A family member c 3013 HIST1H2AD histone cluster 1 H2A family member d 3012 HIST1H2AE histone cluster 1 H2A family member e 8969 HIST1H2AG histone cluster 1 H2A family member g 85235 HIST1H2AH histone cluster 1 H2A family member h 8329 HIST1H2AI histone cluster 1 H2A family member i 8331 HIST1H2AJ histone cluster 1 H2A family member j 8330 HIST1H2AK histone cluster 1 H2A family member k 8332 HIST1H2AL histone cluster 1 H2A family member l 8336 HIST1H2AM histone cluster 1 H2A family member m 255626 HIST1H2BA histone cluster 1 H2B family member a 3018 HIST1H2BB histone cluster 1 H2B family member b 8347 HIST1H2BC histone cluster 1 H2B family member c 3017 HIST1H2BD histone cluster 1 H2B family member d 8345 HIST1H2BH histone cluster 1 H2B family member h 8346 HIST1H2BI histone cluster 1 H2B family member i 8970 HIST1H2BJ histone cluster 1 H2B family member j 85236 HIST1H2BK histone cluster 1 H2B family member k 8340 HIST1H2BL histone cluster 1 H2B family member l 8342 HIST1H2BM histone cluster 1 H2B family member m 8341 HIST1H2BN histone cluster 1 H2B family member n 8348 HIST1H2BO histone cluster 1 H2B family member o 8337 HIST2H2AA3 histone cluster 2 H2A family member a3 723790 HIST2H2AA4 histone cluster 2 H2A family member a4 317772 HIST2H2AB histone cluster 2 H2A family member b 8338 HIST2H2AC histone cluster 2 H2A family member c 8349 HIST2H2BE histone cluster 2 H2B family member e 92815 HIST3H2A histone cluster 3 H2A 128312 HIST3H2BB histone cluster 3 H2B family member b

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 1.77e-01 3.04e-54 Reactome Packaging Of Telomere Ends Cell Cycle 1.07e-01 3.07e-56 Reactome HDACs deacetylate histones Chromatin organization 9.86e-02 1.39e-64 GO nucleosome cellular_component 9.23e-02 4.73e-24 Reactome Metalloprotease DUBs Metabolism of proteins 8.94e-02 7.95e-54 Reactome DNA methylation Gene expression (Transcription) 5.58e-02 1.10e-52 Reactome SIRT1 negatively regulates rRNA expression Gene expression (Transcription) 4.88e-02 4.77e-53 Reactome Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 Signal Transduction 2.37e-02 5.39e-49 Reactome HATs acetylate histones Chromatin organization 1.21e-02 4.42e-48 Reactome Nucleosome assembly Cell Cycle 1.12e-02 4.42e-48 Reactome Deposition of new CENPA-containing nucleosomes at the centromere Cell Cycle 7.03e-03 9.76e-42 Reactome Ub-specific processing proteases Metabolism of proteins 4.58e-03 8.98e-51 Reactome Condensation of Prophase Chromosomes Cell Cycle

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 protein-DNA complex assembly 0.00e+00 0.00e+00 chromatin assembly or disassembly 0.00e+00 0.00e+00 chromatin organization 0.00e+00 0.00e+00 DNA packaging 0.00e+00 0.00e+00 nucleosome assembly 0.00e+00 0.00e+00 nucleosome organization 0.00e+00 0.00e+00 chromatin assembly 0.00e+00 0.00e+00 DNA conformation change 0.00e+00 0.00e+00 gene silencing 0.00e+00 0.00e+00 negative regulation of gene expression, epigenetic 0.00e+00 0.00e+00 chromatin silencing 0.00e+00 0.00e+00 regulation of gene expression, epigenetic 0.00e+00 0.00e+00 protein-DNA complex 0.00e+00 0.00e+00 nucleosome 0.00e+00 0.00e+00 chromatin 0.00e+00 0.00e+00 nuclear chromatin 0.00e+00 0.00e+00 nuclear chromosome 0.00e+00 0.00e+00 protein heterodimerization activity 2.97e-09 2.08e-06 protein ubiquitination 8.44e-09 5.53e-06 protein modification by small protein conjugation

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 CELL CYCLE 0e+00 0e+00 MEIOTIC RECOMBINATION 0e+00 0e+00 RNA POL I PROMOTER OPENING 0e+00 0e+00 MEIOTIC SYNAPSIS 0e+00 0e+00 RNA POL I TRANSCRIPTION 0e+00 0e+00 TELOMERE MAINTENANCE 0e+00 0e+00 CHROMOSOME MAINTENANCE 0e+00 0e+00 PACKAGING OF TELOMERE ENDS 0e+00 0e+00 TRANSCRIPTION 0e+00 0e+00 AMYLOIDS 0e+00 0e+00 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 0e+00 0e+00 MEIOSIS 0e+00 0e+00 DEPOSITION OF NEW CENPA CONTAINING NUCLEOSOMES AT THE CENTROMERE 0e+00 0e+00 MEIOTIC RECOMBINATION 0e+00 0e+00 RNA POL I PROMOTER OPENING 0e+00 0e+00 MEIOTIC SYNAPSIS 0e+00 0e+00 TRANSCRIPTION 0e+00 0e+00 RNA POL I TRANSCRIPTION 0e+00 0e+00 AMYLOIDS 0e+00 0e+00 TELOMERE MAINTENANCE

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 impaired olfaction 1.88e-03 1e+00 abnormal olfactory sensory neuron morphology 5.12e-03 1e+00 hepatic steatosis 5.32e-03 1e+00 decreased neuron apoptosis 1.89e-02 1e+00 taste/olfaction phenotype

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

²FDR corrected p-value (Benjamini-Hochberg)