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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod153

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod153 Module size 60 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 166 AES amino-terminal enhancer of split 56751 BARHL1 BarH like homeobox 1 310704 BCL9 B-cell CLL/lymphoma 9 283149 BCL9L B cell CLL/lymphoma 9 like 127254 C1orf173 glutamate rich 3 140688 C20orf112 nucleolar protein 4 like 9139 CBFA2T2 CBFA2/RUNX1 translocation partner 2 1487 CTBP1 C-terminal binding protein 1 1488 CTBP2 C-terminal binding protein 2 63948 DMRTB1 DMRT like family B with proline rich C-terminal 1 84915 FAM222A family with sequence similarity 222 member A 55731 FAM222B family with sequence similarity 222 member B 3280 HES1 hes family bHLH transcription factor 1 388585 HES5 hes family bHLH transcription factor 5 84667 HES7 hes family bHLH transcription factor 7 23462 HEY1 hes related family bHLH transcription factor with YRPW motif 1 23493 HEY2 hes related family bHLH transcription factor with YRPW motif 2 26508 HEYL hes related family bHLH transcription factor with YRPW motif-like 6927 HNF1A HNF1 homeobox A 386684 KRTAP12-4 keratin associated protein 12-4 51176 LEF1 lymphoid enhancer binding factor 1 9794 MAML1 mastermind like transcriptional coactivator 1 84441 MAML2 mastermind like transcriptional coactivator 2 55534 MAML3 mastermind like transcriptional coactivator 3 4221 MEN1 menin 1 4487 MSX1 msh homeobox 1 4488 MSX2 msh homeobox 2 84504 NKX6-2 NK6 homeobox 2 157848 NKX6-3 NK6 homeobox 3 51701 NLK nemo like kinase 8715 NOL4 nucleolar protein 4 283310 OTOGL otogelin like 5079 PAX5 paired box 5 5083 PAX9 paired box 9 26108 PYGO1 pygopus family PHD finger 1 90780 PYGO2 pygopus family PHD finger 2 10742 RAI2 retinoic acid induced 2 3516 RBPJ recombination signal binding protein for immunoglobulin kappa J region 64864 RFX7 regulatory factor X7 864 RUNX3 runt related transcription factor 3 83482 SCRT1 scratch family transcriptional repressor 1 85508 SCRT2 scratch family transcriptional repressor 2 6591 SNAI2 snail family transcriptional repressor 2 333929 SNAI3 snail family transcriptional repressor 3 64321 SOX17 SRY-box 17 6862 T T-box transcription factor T 6886 TAL1 TAL bHLH transcription factor 1, erythroid differentiation factor 6932 TCF7 transcription factor 7 83439 TCF7L1 transcription factor 7 like 1 6934 TCF7L2 transcription factor 7 like 2 7088 TLE1 transducin like enhancer of split 1 7089 TLE2 transducin like enhancer of split 2 7090 TLE3 transducin like enhancer of split 3 7091 TLE4 transducin like enhancer of split 4 79816 TLE6 transducin like enhancer of split 6 30012 TLX3 T cell leukemia homeobox 3 27287 VENTX VENT homeobox 170261 ZCCHC12 zinc finger CCHC-type containing 12 57507 ZNF608 zinc finger protein 608 79755 ZNF750 zinc finger protein 750

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 3.91e-01 2.28e-26 Reactome Repression of WNT target genes Signal Transduction 3.07e-01 5.11e-18 Reactome NOTCH4 Intracellular Domain Regulates Transcription Signal Transduction 2.38e-01 1.82e-16 GO beta-catenin-TCF complex cellular_component 2.09e-01 2.62e-08 Reactome TCF7L2 mutants don't bind CTBP Disease 1.79e-01 1.63e-10 GO epithelial to mesenchymal transition involved in endocardial cushion formation biological_process 9.46e-02 1.65e-28 Reactome Deactivation of the beta-catenin transactivating complex Signal Transduction 7.83e-02 5.21e-13 Reactome NOTCH2 intracellular domain regulates transcription Signal Transduction 7.12e-02 3.00e-11 GO sequence-specific double-stranded DNA binding molecular_function 5.82e-02 2.03e-17 Reactome NOTCH3 Intracellular Domain Regulates Transcription Signal Transduction 5.73e-02 2.30e-26 GO beta-catenin-TCF complex assembly biological_process 4.88e-02 7.31e-08 GO negative regulation of transcription regulatory region DNA binding biological_process 3.26e-02 2.80e-07 GO signal transduction involved in regulation of gene expression biological_process 2.48e-02 1.68e-12 Reactome RUNX3 regulates NOTCH signaling Gene expression (Transcription) 2.06e-02 9.06e-03 Reactome RUNX3 regulates RUNX1-mediated transcription Gene expression (Transcription) 1.37e-02 5.82e-04 GO regulation of neuron migration biological_process 1.38e-03 1.16e-11 Reactome RUNX3 regulates WNT signaling 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 beta-catenin-TCF complex assembly 0.00e+00 0.00e+00 RNA polymerase II transcription factor activity, sequence-specific DNA binding 6.31e-18 6.01e-15 negative regulation of transcription from RNA polymerase II promoter 7.26e-10 5.50e-07 Wnt signaling pathway 1.03e-09 7.67e-07 Notch signaling pathway 2.10e-09 1.06e-06 transcription regulatory region DNA binding 2.12e-09 1.07e-06 regulatory region DNA binding 5.74e-09 2.34e-06 nuclear chromatin 7.44e-09 3.45e-06 transcription factor binding 8.83e-09 4.07e-06 double-stranded DNA binding 1.52e-08 9.67e-06 epithelial to mesenchymal transition involved in endocardial cushion formation 2.60e-08 1.11e-05 transcription factor activity, protein binding 3.58e-08 2.16e-05 cardiac epithelial to mesenchymal transition 1.04e-07 5.86e-05 positive regulation of transcription of Notch receptor target 1.31e-07 7.25e-05 endocardial cushion formation 1.43e-07 4.72e-05 transcription factor complex 2.82e-07 8.95e-05 nuclear chromosome 2.89e-07 1.51e-04 canonical Wnt signaling pathway 3.53e-07 1.82e-04 epithelial to mesenchymal transition 5.97e-07 1.81e-04 chromatin

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 NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION 0.00e+00 0.00e+00 SIGNALING BY NOTCH 0.00e+00 0.00e+00 SIGNALING BY NOTCH1 0.00e+00 0.00e+00 NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION 0.00e+00 0.00e+00 SIGNALING BY NOTCH 0.00e+00 0.00e+00 SIGNALING BY NOTCH1 2.01e-08 4.27e-06 NOTCH HLH TRANSCRIPTION PATHWAY 2.34e-07 5.78e-05 NOTCH HLH TRANSCRIPTION PATHWAY 6.68e-07 1.19e-04 PRE NOTCH TRANSCRIPTION AND TRANSLATION 3.83e-06 7.81e-04 PRE NOTCH TRANSCRIPTION AND TRANSLATION 6.48e-06 9.98e-04 PRE NOTCH EXPRESSION AND PROCESSING 1.22e-05 1.79e-03 REGULATION OF BETA CELL DEVELOPMENT 3.82e-05 6.56e-03 PRE NOTCH EXPRESSION AND PROCESSING 2.62e-04 3.64e-02 REGULATION OF BETA CELL DEVELOPMENT 6.36e-03 5.57e-01 GENERIC TRANSCRIPTION PATHWAY 4.16e-02 1.00e+00 REGULATION OF GENE EXPRESSION IN BETA CELLS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.27e-06 1.04e-02 absent alveolar process 1.51e-05 6.24e-02 absent molars 4.65e-05 1.36e-01 enlarged pituitary gland 3.23e-04 4.71e-01 increased vestibular hair cell number 4.23e-04 5.51e-01 absent incisors 8.97e-04 8.46e-01 abnormal intestinal enteroendocrine cell morphology 1.16e-03 9.82e-01 arrest of tooth development 1.77e-03 1.00e+00 growth retardation of molars 2.07e-03 1.00e+00 abnormal cell differentiation 2.47e-03 1.00e+00 incomplete somite formation 2.70e-03 1.00e+00 embryonic lethality 3.44e-03 1.00e+00 abnormal pancreas development 3.59e-03 1.00e+00 absent teeth 3.64e-03 1.00e+00 abnormal hair follicle development 3.87e-03 1.00e+00 absent maxillary shelf 4.46e-03 1.00e+00 small intestinal inflammation 4.78e-03 1.00e+00 absent palatine bone horizontal plate 5.99e-03 1.00e+00 abnormal bile duct development 6.12e-03 1.00e+00 abnormal vascular regression 6.84e-03 1.00e+00 abnormal cardiac epithelial to mesenchymal transition

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

²FDR corrected p-value (Benjamini-Hochberg)