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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod298

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod298 Module size 43 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 1820 ARID3A AT-rich interaction domain 3A 10620 ARID3B AT-rich interaction domain 3B 138715 ARID3C AT-rich interaction domain 3C 10865 ARID5A AT-rich interaction domain 5A 546 ATRX ATRX, chromatin remodeler 11177 BAZ1A bromodomain adjacent to zinc finger domain 1A 9031 BAZ1B bromodomain adjacent to zinc finger domain 1B 11176 BAZ2A bromodomain adjacent to zinc finger domain 2A 29994 BAZ2B bromodomain adjacent to zinc finger domain 2B 2186 BPTF bromodomain PHD finger transcription factor 6046 BRD2 bromodomain containing 2 8019 BRD3 bromodomain containing 3 54014 BRWD1 bromodomain and WD repeat domain containing 1 9044 BTAF1 B-TFIID TATA-box binding protein associated factor 1 124773 C17orf64 chromosome 17 open reading frame 64 1105 CHD1 chromodomain helicase DNA binding protein 1 9557 CHD1L chromodomain helicase DNA binding protein 1 like 1826 CHD2 DS cell adhesion molecule 288233 CHD5 tryptophan rich basic protein 84181 CHD6 chromodomain helicase DNA binding protein 6 55636 CHD7 chromodomain helicase DNA binding protein 7 347918 EP400NL EP400 pseudogene 1 375748 ERCC6L2 ERCC excision repair 6 like 2 6596 HLTF helicase like transcription factor 10363 HMG20A high mobility group 20A 10362 HMG20B high mobility group 20B 3148 HMGB2 high mobility group box 2 3149 HMGB3 high mobility group box 3 127540 HMGB4 high mobility group box 4 10042 HMGXB4 HMG-box containing 4 126321 MFSD12 major facilitator superfamily domain containing 12 23132 RAD54L2 RAD54 like 2 257218 SHPRH SNF2 histone linker PHD RING helicase 6594 SMARCA1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 8467 SMARCA5 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 56916 SMARCAD1 SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 6830 SUPT6H SPT6 homolog, histone chaperone 7019 TFAM transcription factor A, mitochondrial 9760 TOX thymocyte selection associated high mobility group box 84969 TOX2 TOX high mobility group box family member 2 27324 TOX3 TOX high mobility group box family member 3 8805 TRIM24 tripartite motif containing 24 84083 ZRANB3 zinc finger RANBP2-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 1.38e-01 7.40e-09 GO nuclear replication fork cellular_component 1.09e-01 1.89e-21 GO helicase activity molecular_function 9.62e-02 2.71e-27 GO chromatin remodeling biological_process 7.02e-02 6.79e-08 GO lysine-acetylated histone binding molecular_function 3.14e-02 2.23e-04 GO negative regulation of protein sumoylation biological_process 2.84e-02 7.20e-06 GO DNA binding, bending molecular_function 2.00e-02 6.80e-03 Reactome Mitochondrial transcription initiation Gene expression (Transcription)

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 DNA metabolic process 0.00e+00 0.00e+00 covalent chromatin modification 0.00e+00 0.00e+00 chromatin organization 0.00e+00 0.00e+00 chromatin remodeling 0.00e+00 0.00e+00 DNA geometric change 0.00e+00 0.00e+00 DNA conformation change 0.00e+00 0.00e+00 histone binding 0.00e+00 0.00e+00 helicase activity 2.07e-10 1.22e-07 nucleoside-triphosphatase activity 2.59e-10 1.26e-07 NURF complex 2.92e-10 1.41e-07 SWI/SNF superfamily-type complex 1.01e-08 6.57e-06 cellular response to DNA damage stimulus 1.57e-08 6.97e-06 lysine-acetylated histone binding 2.20e-08 8.33e-06 chromatin 2.25e-08 1.40e-05 DNA repair 2.68e-08 1.65e-05 nucleosome organization 4.09e-08 1.67e-05 chromatin binding 7.36e-08 2.89e-05 DNA-dependent ATPase activity 2.47e-07 7.89e-05 heterochromatin 8.69e-07 4.19e-04 chromatin assembly or disassembly

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.30e-03 3.25e-01 SIGNALING BY FGFR1 MUTANTS 3.30e-03 3.25e-01 SIGNALING BY FGFR1 FUSION MUTANTS 3.31e-03 3.26e-01 SIGNALING BY FGFR MUTANTS 5.51e-03 4.95e-01 SIGNALING BY FGFR IN DISEASE 7.51e-03 5.80e-01 APOPTOSIS INDUCED DNA FRAGMENTATION 9.66e-03 7.14e-01 SIGNALING BY FGFR1 FUSION MUTANTS 9.68e-03 7.14e-01 SIGNALING BY FGFR1 MUTANTS 9.71e-03 7.15e-01 SIGNALING BY FGFR MUTANTS 1.29e-02 9.73e-01 DEPOSITION OF NEW CENPA CONTAINING NUCLEOSOMES AT THE CENTROMERE 1.39e-02 1.00e+00 APOPTOSIS INDUCED DNA FRAGMENTATION 1.50e-02 1.00e+00 SIGNALING BY FGFR IN DISEASE 1.78e-02 1.00e+00 DEPOSITION OF NEW CENPA CONTAINING NUCLEOSOMES AT THE CENTROMERE 2.28e-02 1.00e+00 CHROMOSOME MAINTENANCE 2.68e-02 1.00e+00 APOPTOTIC EXECUTION PHASE 2.73e-02 1.00e+00 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 2.76e-02 1.00e+00 TRANSCRIPTION 3.03e-02 1.00e+00 APOPTOTIC EXECUTION PHASE 3.38e-02 1.00e+00 CHROMOSOME MAINTENANCE 3.89e-02 1.00e+00 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 3.95e-02 1.00e+00 TRANSCRIPTION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.04e-05 1.24e-01 aorta coarctation 5.78e-04 6.61e-01 abnormal neuronal precursor proliferation 1.37e-03 1.00e+00 increased apoptosis 3.07e-03 1.00e+00 teratozoospermia 5.12e-03 1.00e+00 decreased birth body size 6.30e-03 1.00e+00 decreased erythroid progenitor cell number 8.18e-03 1.00e+00 decreased fetal size 9.20e-03 1.00e+00 increased carbon dioxide production 9.38e-03 1.00e+00 abnormal CD4-positive, CD25-positive, alpha-beta regulatory T cell morphology 1.01e-02 1.00e+00 embryonic growth arrest 1.05e-02 1.00e+00 abnormal male germ cell morphology 1.06e-02 1.00e+00 abnormal telencephalon development 1.12e-02 1.00e+00 abnormal stapes footplate morphology 1.12e-02 1.00e+00 abnormal inner ear canal fusion 1.12e-02 1.00e+00 decreased T-helper 17 cell number 1.13e-02 1.00e+00 abnormal vestibular nerve morphology 1.13e-02 1.00e+00 aortic arch coarctation 1.31e-02 1.00e+00 abnormal epigenetic regulation of gene expression 1.31e-02 1.00e+00 decreased circulating bilirubin level 1.31e-02 1.00e+00 keratoconjunctivitis sicca

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

²FDR corrected p-value (Benjamini-Hochberg)