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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod162

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod162 Module size 23 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 64431 ACTR6 ARP6 actin related protein 6 homolog 7862 BRPF1 bromodomain and PHD finger containing 1 10428 CFDP1 craniofacial development protein 1 298447 DMAP1 DNA methyltransferase 1-associated protein 1 57634 EP400 E1A binding protein p400 80314 EPC1 enhancer of polycomb homolog 1 26122 EPC2 enhancer of polycomb homolog 2 54556 ING3 inhibitor of growth family member 3 51147 ING4 inhibitor of growth family member 4 84289 ING5 inhibitor of growth family member 5 54617 INO80 INO80 complex subunit 64769 MEAF6 MYST/Esa1 associated factor 6 10933 MORF4L1 mortality factor 4 like 1 9643 MORF4L2 mortality factor 4 like 2 55257 MRGBP MRG domain binding protein 10943 MSL3 MSL complex subunit 3 79960 PHF17 jade family PHD finger 1 8607 RUVBL1 RuvB like AAA ATPase 1 10856 RUVBL2 RuvB like AAA ATPase 2 10847 SRCAP Snf2 related CREBBP activator protein 6944 VPS72 vacuolar protein sorting 72 homolog 8089 YEATS4 YEATS domain containing 4 10467 ZNHIT1 zinc finger HIT-type containing 1

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 2.82e-01 8.73e-33 GO NuA4 histone acetyltransferase complex cellular_component 2.24e-01 3.21e-30 GO histone H2A acetylation biological_process 1.35e-01 6.36e-08 GO MOZ/MORF histone acetyltransferase complex cellular_component 1.18e-01 1.52e-07 GO histone exchange biological_process 6.15e-02 1.54e-18 GO Swr1 complex cellular_component 8.74e-03 1.35e-31 Reactome HATs acetylate histones Chromatin organization

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 histone H4 acetylation 0.00e+00 0.00e+00 covalent chromatin modification 0.00e+00 0.00e+00 histone H2A acetylation 0.00e+00 0.00e+00 internal protein amino acid acetylation 0.00e+00 0.00e+00 protein acetylation 0.00e+00 0.00e+00 chromatin organization 0.00e+00 0.00e+00 chromatin remodeling 0.00e+00 0.00e+00 peptidyl-lysine acetylation 0.00e+00 0.00e+00 internal peptidyl-lysine acetylation 0.00e+00 0.00e+00 histone modification 0.00e+00 0.00e+00 histone acetylation 0.00e+00 0.00e+00 peptidyl-lysine modification 0.00e+00 0.00e+00 regulation of growth 0.00e+00 0.00e+00 transferase complex 0.00e+00 0.00e+00 NuA4 histone acetyltransferase complex 0.00e+00 0.00e+00 histone acetyltransferase complex 1.67e-11 9.22e-09 Swr1 complex 3.53e-08 1.30e-05 SWI/SNF superfamily-type complex 1.25e-07 4.19e-05 Piccolo NuA4 histone acetyltransferase complex 7.63e-07 2.47e-04 methylated histone binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 8.09e-06 1.23e-03 EXTENSION OF TELOMERES 8.46e-06 1.28e-03 TELOMERE MAINTENANCE 3.40e-05 5.90e-03 EXTENSION OF TELOMERES 6.25e-05 1.02e-02 TELOMERE MAINTENANCE 1.09e-04 1.38e-02 CHROMOSOME MAINTENANCE 4.70e-04 6.10e-02 CHROMOSOME MAINTENANCE 4.75e-03 4.38e-01 CELL CYCLE 4.88e-03 4.02e-01 DEPOSITION OF NEW CENPA CONTAINING NUCLEOSOMES AT THE CENTROMERE 1.03e-02 8.15e-01 DEPOSITION OF NEW CENPA CONTAINING NUCLEOSOMES AT THE CENTROMERE

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 absent erythrocytes 1.88e-03 1e+00 liver vascular congestion 3.75e-03 1e+00 pulmonary vascular congestion 5.61e-03 1e+00 visceral vascular congestion 7.50e-03 1e+00 thin skin 9.38e-03 1e+00 skin edema 1.25e-02 1e+00 increased thymocyte number 1.49e-02 1e+00 disorganized myocardium 1.50e-02 1e+00 abnormal muscle development 1.86e-02 1e+00 belly spot 1.93e-02 1e+00 complete lethality 2.05e-02 1e+00 decreased circulating magnesium level 2.05e-02 1e+00 abnormal chemokine level 2.23e-02 1e+00 wavy neural tube 2.43e-02 1e+00 decreased double-positive T cell number 2.55e-02 1e+00 increased circulating interleukin-6 level 2.78e-02 1e+00 decreased circulating sodium level 2.79e-02 1e+00 abnormal epidermis stratum basale morphology 2.80e-02 1e+00 abnormal class switch recombination 2.91e-02 1e+00 decreased circulating amylase level

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

²FDR corrected p-value (Benjamini-Hochberg)