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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod238

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod238 Module size 53 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 196528 ARID2 AT-rich interaction domain 2 5926 ARID4A AT-rich interaction domain 4A 51742 ARID4B AT-rich interaction domain 4B 55870 ASH1L ASH1 like histone lysine methyltransferase 23774 BRD1 bromodomain containing 1 299347 BRF1 BRF1, RNA polymerase III transcription initiation factor subunit 55290 BRF2 BRF2, RNA polymerase III transcription initiation factor subunit 27154 BRPF3 bromodomain and PHD finger containing 3 27443 CECR2 CECR2, histone acetyl-lysine reader 1459 CSNK2A2 casein kinase 2 alpha 2 10664 CTCF CCCTC-binding factor 79813 EHMT1 euchromatic histone lysine methyltransferase 1 2623 GATA1 GATA binding protein 1 2624 GATA2 GATA binding protein 2 2625 GATA3 GATA binding protein 3 140628 GATA5 GATA binding protein 5 2627 GATA6 GATA binding protein 6 2959 GTF2B general transcription factor IIB 2971 GTF3A general transcription factor IIIA 10320 IKZF1 IKAROS family zinc finger 1 22807 IKZF2 IKAROS family zinc finger 2 64375 IKZF4 IKAROS family zinc finger 4 2648 KAT2A lysine acetyltransferase 2A 8850 KAT2B lysine acetyltransferase 2B 10524 KAT5 lysine acetyltransferase 5 7994 KAT6A lysine acetyltransferase 6A 23522 KAT6B lysine acetyltransferase 6B 11143 KAT7 lysine acetyltransferase 7 84148 KAT8 lysine acetyltransferase 8 4801 NFYB nuclear transcription factor Y subunit beta 4802 NFYC nuclear transcription factor Y subunit gamma 8438 RAD54L RAD54 like 25942 SIN3A SIN3 transcription regulator family member A 23309 SIN3B SIN3 transcription regulator family member B 6597 SMARCA4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 93624 TADA2B transcriptional adaptor 2B 6872 TAF1 TATA-box binding protein associated factor 1 138474 TAF1L TATA-box binding protein associated factor 1 like 6873 TAF2 TATA-box binding protein associated factor 2 83860 TAF3 TATA-box binding protein associated factor 3 117526 TBP TATA box binding protein 9519 TBPL1 TATA-box binding protein like 1 387332 TBPL2 TATA-box binding protein like 2 146845 WDR16 cilia and flagella associated protein 52 401551 WDR38 WD repeat domain 38 54554 WDR5B WD repeat domain 5B 58525 WIZ widely interspaced zinc finger motifs 55884 WSB2 WD repeat and SOCS box containing 2 161882 ZFPM1 zinc finger protein, FOG family member 1 23414 ZFPM2 zinc finger protein, FOG family member 2 7561 ZNF14 zinc finger protein 14 7702 ZNF143 zinc finger protein 143 25925 ZNF521 zinc finger protein 521

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 2.64e-01 2.03e-09 GO MOZ/MORF histone acetyltransferase complex cellular_component 1.78e-01 1.20e-10 GO anatomical structure formation involved in morphogenesis biological_process 1.41e-01 3.08e-12 GO acetyltransferase activity molecular_function 9.48e-02 1.21e-08 GO H4 histone acetyltransferase activity molecular_function 7.28e-02 6.53e-10 GO transcription factor activity, RNA polymerase II transcription factor binding molecular_function 7.14e-02 3.89e-09 GO RNA polymerase II core promoter sequence-specific DNA binding molecular_function 6.98e-02 9.24e-10 GO tissue development biological_process 6.31e-02 1.73e-13 GO transcription factor TFIID complex cellular_component 6.04e-02 4.71e-06 GO regulation of transcription by RNA polymerase III biological_process 5.53e-02 1.01e-16 GO histone acetyltransferase activity molecular_function 2.85e-02 3.54e-06 GO transcription factor activity, RNA polymerase II core promoter sequence-specific binding involved in preinitiation complex assembly molecular_function 2.81e-02 1.19e-04 GO transcription factor TFIIA complex cellular_component 1.66e-02 1.73e-05 GO lysine-acetylated histone binding molecular_function 1.43e-02 4.12e-07 GO TBP-class protein binding molecular_function 1.06e-02 5.40e-08 Reactome RNA Polymerase III Transcription Gene expression (Transcription) 1.04e-02 5.40e-08 Reactome RNA Polymerase III Abortive And Retractive Initiation Gene expression (Transcription) 1.02e-02 3.01e-09 GO RNA polymerase II transcriptional preinitiation complex assembly biological_process 1.02e-02 4.95e-06 GO histone deacetylase activity molecular_function 8.80e-03 1.19e-05 GO embryonic hemopoiesis biological_process 6.72e-03 5.40e-08 Reactome RNA Polymerase III Transcription Initiation Gene expression (Transcription) 4.03e-03 9.69e-06 GO C2H2 zinc finger domain binding molecular_function 2.82e-03 3.04e-18 Reactome Chromatin modifying enzymes Chromatin organization 2.46e-03 3.04e-18 Reactome Chromatin organization Chromatin organization 1.33e-03 5.17e-04 GO rRNA transcription 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 0.00e+00 0.00e+00 transcription from RNA polymerase II promoter 0.00e+00 0.00e+00 chromatin organization 0.00e+00 0.00e+00 histone modification 0.00e+00 0.00e+00 peptidyl-lysine modification 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 internal protein amino acid acetylation 0.00e+00 0.00e+00 protein acetylation 0.00e+00 0.00e+00 histone acetylation 0.00e+00 0.00e+00 transcription factor complex 0.00e+00 0.00e+00 nuclear transcription factor complex 0.00e+00 0.00e+00 histone acetyltransferase complex 0.00e+00 0.00e+00 transcription factor binding 3.69e-21 3.57e-18 covalent chromatin modification 5.98e-12 3.38e-09 RNA polymerase II transcription factor complex 1.65e-10 1.34e-07 DNA-templated transcription, initiation 1.98e-10 9.86e-08 transferase complex 3.03e-10 1.75e-07 histone acetyltransferase activity 3.17e-10 1.83e-07 peptide-lysine-N-acetyltransferase activity 4.51e-10 3.50e-07 histone H3 acetylation

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 7.07e-08 1.86e-05 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 5.76e-07 1.04e-04 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 1.24e-05 1.82e-03 TRANSCRIPTION 1.47e-05 2.14e-03 RNA POL III TRANSCRIPTION 1.66e-05 3.06e-03 RNA POL III TRANSCRIPTION 7.85e-05 1.02e-02 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 8.19e-05 1.30e-02 TRANSCRIPTION 1.82e-04 2.64e-02 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 2.32e-04 2.71e-02 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 3 PROMOTER 3.21e-04 4.36e-02 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 3 PROMOTER 4.91e-04 6.33e-02 RNA POL II TRANSCRIPTION PRE INITIATION AND PROMOTER OPENING 5.66e-04 6.05e-02 RNA POL II TRANSCRIPTION PRE INITIATION AND PROMOTER OPENING 6.12e-04 6.48e-02 NOTCH HLH TRANSCRIPTION PATHWAY 1.95e-03 1.82e-01 RNA POL II PRE TRANSCRIPTION EVENTS 2.26e-03 2.37e-01 RNA POL II PRE TRANSCRIPTION EVENTS 2.42e-03 2.51e-01 NOTCH HLH TRANSCRIPTION PATHWAY 3.22e-03 2.83e-01 PRE NOTCH TRANSCRIPTION AND TRANSLATION 5.06e-03 4.62e-01 PRE NOTCH TRANSCRIPTION AND TRANSLATION 5.25e-03 4.28e-01 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 2 PROMOTER 5.35e-03 4.34e-01 NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.20e-07 2.70e-03 decreased erythroid progenitor cell number 1.78e-06 1.34e-02 increased erythroid progenitor cell number 2.21e-06 1.57e-02 abnormal definitive hematopoiesis 3.22e-06 2.10e-02 small liver 3.32e-05 1.09e-01 abnormal erythropoiesis 7.09e-05 1.80e-01 impaired hematopoiesis 2.15e-04 3.64e-01 abnormal megakaryocyte progenitor cell morphology 2.95e-04 4.44e-01 liver hypoplasia 3.81e-04 5.19e-01 pallor 4.19e-04 5.47e-01 abnormal embryonic erythropoiesis 5.18e-04 6.19e-01 abnormal common myeloid progenitor cell morphology 6.97e-04 7.33e-01 increased embryonic tissue cell apoptosis 7.64e-04 7.68e-01 abnormal chromosome morphology 1.07e-03 9.34e-01 genetic imprinting 1.23e-03 1.00e+00 increased mean platelet volume 1.49e-03 1.00e+00 myelofibrosis 1.68e-03 1.00e+00 abnormal erythroid progenitor cell morphology 1.94e-03 1.00e+00 decreased double-negative T cell number 2.01e-03 1.00e+00 anemia 2.14e-03 1.00e+00 overriding aortic valve

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

²FDR corrected p-value (Benjamini-Hochberg)