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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod109

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod109 Module size 37 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 158983 H2BFWT H2B histone family member W, testis specific 3020 H3F3A H3 histone family member 3A 3021 H3F3B H3 histone family member 3B 440093 H3F3C H3 histone family member 3C 8344 HIST1H2BE histone cluster 1 H2B family member e 8343 HIST1H2BF histone cluster 1 H2B family member f 8339 HIST1H2BG histone cluster 1 H2B family member g 8358 HIST1H3B histone cluster 1 H3 family member b 8352 HIST1H3C histone cluster 1 H3 family member c 8351 HIST1H3D histone cluster 1 H3 family member d 8353 HIST1H3E histone cluster 1 H3 family member e 8968 HIST1H3F histone cluster 1 H3 family member f 8355 HIST1H3G histone cluster 1 H3 family member g 8357 HIST1H3H histone cluster 1 H3 family member h 8354 HIST1H3I histone cluster 1 H3 family member i 8356 HIST1H3J histone cluster 1 H3 family member j 8359 HIST1H4A histone cluster 1 H4 family member a 8366 HIST1H4B histone cluster 1 H4 family member b 8364 HIST1H4C histone cluster 1 H4 family member c 8360 HIST1H4D histone cluster 1 H4 family member d 8367 HIST1H4E histone cluster 1 H4 family member e 8361 HIST1H4F histone cluster 1 H4 family member f 8369 HIST1H4G histone cluster 1 H4 family member g 8365 HIST1H4H histone cluster 1 H4 family member h 8294 HIST1H4I histone cluster 1 H4 family member i 8363 HIST1H4J histone cluster 1 H4 family member j 8362 HIST1H4K histone cluster 1 H4 family member k 8368 HIST1H4L histone cluster 1 H4 family member l 440689 HIST2H2BF histone cluster 2 H2B family member f 333932 HIST2H3A histone cluster 2 H3 family member a 126961 HIST2H3C histone cluster 2 H3 family member c 653604 HIST2H3D histone cluster 2 H3 family member d 8370 HIST2H4A histone cluster 2 H4 family member a 554313 HIST2H4B histone cluster 2 H4 family member b 121504 HIST4H4 histone cluster 4 H4 6749 SSRP1 structure specific recognition protein 1 11198 SUPT16H SPT16 homolog, facilitates chromatin remodeling subunit

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 7.69e-02 2.18e-08 GO chromatin silencing at rDNA biological_process 1.31e-02 2.20e-15 GO nucleosome assembly biological_process 1.02e-02 2.56e-13 GO nucleosome 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 nucleosome organization 0.00e+00 0.00e+00 nucleosome 7.96e-12 7.19e-09 chromatin assembly or disassembly 1.01e-11 5.65e-09 protein-DNA complex 5.16e-10 2.87e-07 protein heterodimerization activity 7.47e-10 5.65e-07 nucleosome assembly 1.24e-09 9.12e-07 chromatin assembly 3.31e-09 2.30e-06 DNA packaging 3.87e-09 2.66e-06 protein-DNA complex assembly 5.58e-09 2.63e-06 histone binding 1.20e-08 4.71e-06 chromatin 1.31e-08 8.40e-06 chromatin organization 1.52e-08 9.67e-06 DNA conformation change 1.76e-08 1.11e-05 chromatin silencing at rDNA 2.79e-07 8.86e-05 nuclear nucleosome 5.55e-07 1.85e-04 nucleosome binding 1.65e-06 5.04e-04 chromatin binding 1.77e-06 8.03e-04 chromatin silencing 2.61e-06 1.14e-03 DNA replication-independent nucleosome organization 4.74e-06 1.97e-03 negative regulation of gene expression, epigenetic

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 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 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 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 9.82e-06 4.66e-02 arrest of spermiogenesis 9.97e-06 4.71e-02 polyploidy 5.54e-05 1.53e-01 abnormal chromosome morphology 5.60e-05 1.54e-01 partial lethality 5.62e-05 1.54e-01 abnormal cell nucleus morphology 1.69e-04 3.17e-01 abnormal cell cycle 1.77e-04 3.24e-01 reduced female fertility 1.68e-02 1.00e+00 inner cell mass degeneration

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

²FDR corrected p-value (Benjamini-Hochberg)