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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod86

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod86 Module size 44 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 6314 ATXN7 ataxin 7 222255 ATXN7L1 ataxin 7 like 1 127002 ATXN7L2 ataxin 7 like 2 56970 ATXN7L3 ataxin 7 like 3 552889 ATXN7L3B ataxin 7 like 3B 112869 CCDC101 SAGA complex associated factor 29 84229 CCDC135 dynein regulatory complex subunit 7 57325 CSRP2BP lysine acetyltransferase 14 1810 DR1 down-regulator of transcription 1 56943 ENY2 ENY2, transcription and export complex 2 subunit 55578 FAM48A SPT20 homolog, SAGA complex component 7918 GPANK1 G-patch domain and ankyrin repeats 1 653656 MBD3L4 methyl-CpG binding domain protein 3 like 4 284428 MBD3L5 methyl-CpG binding domain protein 3 like 5 51562 MBIP MAP3K12 binding inhibitory protein 1 79595 SAP130 Sin3A associated protein 130 391253 SPINT3 serine peptidase inhibitor, Kunitz type 4 8464 SUPT3H SPT3 homolog, SAGA and STAGA complex component 9913 SUPT7L SPT7 like, STAGA complex gamma subunit 26022 TADA1 transmembrane protein 98 6871 TADA2A transcriptional adaptor 2A 10474 TADA3 transcriptional adaptor 3 6881 TAF10 TATA-box binding protein associated factor 10 6882 TAF11 TATA-box binding protein associated factor 11 6883 TAF12 TATA-box binding protein associated factor 12 6884 TAF13 TATA-box binding protein associated factor 13 140932 TAF4 BCL2 interacting protein 1 6875 TAF4B TATA-box binding protein associated factor 4b 6877 TAF5 TATA-box binding protein associated factor 5 27097 TAF5L TATA-box binding protein associated factor 5 like 6878 TAF6 TATA-box binding protein associated factor 6 10629 TAF6L TATA-box binding protein associated factor 6 like 6879 TAF7 TATA-box binding protein associated factor 7 54457 TAF7L TATA-box binding protein associated factor 7 like 129685 TAF8 TATA-box binding protein associated factor 8 6880 TAF9 TATA-box binding protein associated factor 9 51616 TAF9B TATA-box binding protein associated factor 9b 23326 USP22 ubiquitin specific peptidase 22 84749 USP30 ubiquitin specific peptidase 30 84101 USP44 ubiquitin specific peptidase 44 25862 USP49 ubiquitin specific peptidase 49 158880 USP51 ubiquitin specific peptidase 51 55689 YEATS2 YEATS domain containing 2 26009 ZZZ3 zinc finger ZZ-type containing 3

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 2.29e-01 3.23e-28 GO transcription factor TFTC complex cellular_component 1.64e-01 2.00e-16 GO histone deubiquitination biological_process 1.52e-01 1.09e-23 GO SAGA complex cellular_component 1.23e-01 7.62e-23 GO STAGA complex cellular_component 1.07e-01 1.44e-31 GO transcription factor TFIID complex cellular_component 9.35e-02 1.97e-22 GO RNA polymerase II transcriptional preinitiation complex assembly biological_process 7.63e-02 1.40e-28 GO histone H3 acetylation biological_process 6.72e-02 8.87e-18 GO DNA-templated transcription, initiation biological_process 3.35e-02 4.51e-33 Reactome HATs acetylate histones Chromatin organization 7.85e-03 3.47e-04 GO methylation-dependent chromatin silencing 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 0e+00 0e+00 regulation of signal transduction by p53 class mediator 0e+00 0e+00 DNA-templated transcription, elongation 0e+00 0e+00 transcription from RNA polymerase II promoter 0e+00 0e+00 DNA-templated transcription, initiation 0e+00 0e+00 transcription initiation from RNA polymerase II promoter 0e+00 0e+00 transcription elongation from RNA polymerase II promoter 0e+00 0e+00 protein modification by small protein removal 0e+00 0e+00 protein deubiquitination 0e+00 0e+00 RNA polymerase II transcriptional preinitiation complex assembly 0e+00 0e+00 covalent chromatin modification 0e+00 0e+00 histone H3 acetylation 0e+00 0e+00 internal protein amino acid acetylation 0e+00 0e+00 protein acetylation 0e+00 0e+00 chromatin organization 0e+00 0e+00 peptidyl-lysine acetylation 0e+00 0e+00 internal peptidyl-lysine acetylation 0e+00 0e+00 histone modification 0e+00 0e+00 histone acetylation 0e+00 0e+00 peptidyl-lysine modification 0e+00 0e+00 histone deubiquitination

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 RNA POL II PRE TRANSCRIPTION EVENTS 0.00e+00 0.00e+00 HIV LIFE CYCLE 0.00e+00 0.00e+00 LATE PHASE OF HIV LIFE CYCLE 0.00e+00 0.00e+00 HIV INFECTION 0.00e+00 0.00e+00 RNA POL II TRANSCRIPTION PRE INITIATION AND PROMOTER OPENING 0.00e+00 0.00e+00 RNA POL II PRE TRANSCRIPTION EVENTS 0.00e+00 0.00e+00 HIV LIFE CYCLE 0.00e+00 0.00e+00 LATE PHASE OF HIV LIFE CYCLE 0.00e+00 0.00e+00 RNA POL II TRANSCRIPTION PRE INITIATION AND PROMOTER OPENING 7.37e-11 2.70e-08 RNA POL II TRANSCRIPTION 8.90e-11 2.44e-08 HIV INFECTION 2.51e-10 6.58e-08 RNA POL II TRANSCRIPTION 4.45e-09 1.35e-06 TRANSCRIPTION 1.06e-08 2.32e-06 TRANSCRIPTION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.84e-04 3.31e-01 preweaning lethality 5.61e-03 1.00e+00 decreased alpha-beta T cell number 5.61e-03 1.00e+00 opacity of vitreous body 7.47e-03 1.00e+00 abnormal trophoblast giant cell proliferation 7.48e-03 1.00e+00 abnormal zygomatic bone morphology 8.70e-03 1.00e+00 embryonic lethality 9.34e-03 1.00e+00 small embryonic epiblast 9.34e-03 1.00e+00 thin retinal inner plexiform layer 1.31e-02 1.00e+00 increased embryonic neuroepithelium apoptosis 1.38e-02 1.00e+00 complete preweaning lethality 1.49e-02 1.00e+00 eyelids fail to open 1.86e-02 1.00e+00 abnormal spermatogonia proliferation 1.86e-02 1.00e+00 abnormal cerebellum vermis morphology 1.86e-02 1.00e+00 abnormal eye size 2.04e-02 1.00e+00 increased hepatoma incidence 2.04e-02 1.00e+00 absent embryonic epiblast 2.05e-02 1.00e+00 decreased NK T cell number 2.05e-02 1.00e+00 decreased post-tetanic potentiation 2.12e-02 1.00e+00 asthenozoospermia 2.12e-02 1.00e+00 decreased fibroblast apoptosis

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

²FDR corrected p-value (Benjamini-Hochberg)