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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod173

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod173 Module size 30 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 51412 ACTL6B actin like 6B 8289 ARID1A AT-rich interaction domain 1A 57492 ARID1B AT-rich interaction domain 1B 9274 BCL7C BCL tumor suppressor 7C 29117 BRD7 bromodomain containing 7 119710 C11orf74 chromosome 11 open reading frame 74 78996 C7orf49 cell cycle regulator of NHEJ 8193 DPF1 double PHD fingers 1 5977 DPF2 double PHD fingers 2 8110 DPF3 double PHD fingers 3 3070 HELLS helicase, lymphoid specific 3146 HMGB1 high mobility group box 1 51603 METTL13 methyltransferase like 13 55193 PBRM1 polybromo 1 55274 PHF10 PHD finger protein 10 5989 RFX1 regulatory factor X1 5990 RFX2 regulatory factor X2 5991 RFX3 regulatory factor X3 5992 RFX4 regulatory factor X4 5993 RFX5 regulatory factor X5 222546 RFX6 regulatory factor X6 731220 RFX8 RFX family member 8, lacking RFX DNA binding domain 6595 SMARCA2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 6598 SMARCB1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 6599 SMARCC1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1 6601 SMARCC2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2 6602 SMARCD1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 6603 SMARCD2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 6605 SMARCE1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 126637 TCHHL1 trichohyalin like 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 4.96e-01 3.20e-33 GO nBAF complex cellular_component 1.24e-01 2.59e-26 GO SWI/SNF complex cellular_component 1.89e-02 4.11e-21 GO npBAF complex cellular_component 1.85e-02 6.23e-19 GO nucleosome disassembly biological_process 8.42e-03 6.75e-24 Reactome RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known 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 covalent chromatin modification 0.00e+00 0.00e+00 chromatin remodeling 0.00e+00 0.00e+00 chromatin organization 0.00e+00 0.00e+00 nucleosome disassembly 0.00e+00 0.00e+00 SWI/SNF complex 0.00e+00 0.00e+00 BAF-type complex 0.00e+00 0.00e+00 npBAF complex 0.00e+00 0.00e+00 nBAF complex 0.00e+00 0.00e+00 SWI/SNF superfamily-type complex 2.63e-11 2.30e-08 chromatin assembly or disassembly 2.17e-10 1.74e-07 ATP-dependent chromatin remodeling 1.14e-09 8.43e-07 nucleosome organization 1.23e-09 6.43e-07 RNA polymerase II core promoter proximal region sequence-specific DNA binding 1.88e-09 9.56e-07 core promoter proximal region sequence-specific DNA binding 2.06e-09 1.04e-06 core promoter proximal region DNA binding 8.76e-09 3.50e-06 nuclear chromatin 1.38e-08 5.37e-06 chromatin 4.32e-08 1.58e-05 nuclear chromosome 5.21e-08 2.09e-05 transcription regulatory region DNA binding 5.24e-08 2.10e-05 regulatory region DNA binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 8.78e-03 7.21e-01 APOPTOSIS INDUCED DNA FRAGMENTATION 1.07e-02 8.40e-01 ADVANCED GLYCOSYLATION ENDPRODUCT RECEPTOR SIGNALING 1.88e-02 1.00e+00 RIP MEDIATED NFKB ACTIVATION VIA DAI 2.21e-02 1.00e+00 TRAF6 MEDIATED NFKB ACTIVATION 2.88e-02 1.00e+00 TAK1 ACTIVATES NFKB BY PHOSPHORYLATION AND ACTIVATION OF IKKS COMPLEX 3.23e-02 1.00e+00 APOPTOTIC EXECUTION PHASE 4.54e-02 1.00e+00 RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 7.62e-04 7.68e-01 abnormal telencephalon morphology 3.74e-03 1.00e+00 Leydig cell hypertrophy 3.75e-03 1.00e+00 abnormal chromosome number 5.62e-03 1.00e+00 increased renal tubule apoptosis 7.47e-03 1.00e+00 absent endoderm 7.98e-03 1.00e+00 ventricular septal defect 9.33e-03 1.00e+00 small floor plate 9.33e-03 1.00e+00 cerebral aqueductal stenosis 9.33e-03 1.00e+00 absent trophectoderm cell proliferation 9.34e-03 1.00e+00 increased brain tumor incidence 9.34e-03 1.00e+00 absent myocardial trabeculae 9.35e-03 1.00e+00 intestinal obstruction 1.12e-02 1.00e+00 mesocardia 1.12e-02 1.00e+00 decreased embryo weight 1.12e-02 1.00e+00 increased trophectoderm apoptosis 1.12e-02 1.00e+00 abnormal optic cup morphology 1.12e-02 1.00e+00 abnormal pluripotent precursor cell morphology/development 1.31e-02 1.00e+00 renal tubular necrosis 1.49e-02 1.00e+00 abnormal lateral ventricle morphology 1.67e-02 1.00e+00 abnormal neural fold elevation formation

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

²FDR corrected p-value (Benjamini-Hochberg)