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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod55

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod55 Module size 55 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 429 ASCL1 achaete-scute family bHLH transcription factor 1 56676 ASCL3 achaete-scute family bHLH transcription factor 3 121549 ASCL4 achaete-scute family bHLH transcription factor 4 647219 ASCL5 achaete-scute family bHLH transcription factor 5 474 ATOH1 atonal bHLH transcription factor 1 220202 ATOH7 atonal bHLH transcription factor 7 84913 ATOH8 atonal bHLH transcription factor 8 27319 BHLHE22 basic helix-loop-helix family member e22 128408 BHLHE23 basic helix-loop-helix family member e23 389799 C9orf171 cilia and flagella associated protein 77 2019 EN1 engrailed homeobox 1 2020 EN2 engrailed homeobox 2 401507 FAM74A1 family with sequence similarity 74 member A1 222894 FERD3L Fer3 like bHLH transcription factor 344018 FIGLA folliculogenesis specific bHLH transcription factor 9421 HAND1 heart and neural crest derivatives expressed 1 9464 HAND2 heart and neural crest derivatives expressed 2 391723 HELT helt bHLH transcription factor 54626 HES2 hes family bHLH transcription factor 2 57801 HES4 hes family bHLH transcription factor 4 55502 HES6 hes family bHLH transcription factor 6 3398 ID2 inhibitor of DNA binding 2 3399 ID3 inhibitor of DNA binding 3, HLH protein 3400 ID4 inhibitor of DNA binding 4, HLH protein 4066 LYL1 LYL1, basic helix-loop-helix family member 55897 MESP1 mesoderm posterior bHLH transcription factor 1 145873 MESP2 mesoderm posterior bHLH transcription factor 2 361807 MSC LEM domain containing 2 343930 MSGN1 mesogenin 1 4617 MYF5 myogenic factor 5 4618 MYF6 myogenic factor 6 4656 MYOG myogenin 4761 NEUROD2 neuronal differentiation 2 58158 NEUROD4 neuronal differentiation 4 4762 NEUROG1 neurogenin 1 63973 NEUROG2 neurogenin 2 50674 NEUROG3 neurogenin 3 4807 NHLH1 nescient helix-loop-helix 1 4808 NHLH2 nescient helix-loop-helix 2 116448 OLIG1 oligodendrocyte transcription factor 1 10215 OLIG2 oligodendrocyte transcription factor 2 167826 OLIG3 oligodendrocyte transcription factor 3 256297 PTF1A pancreas associated transcription factor 1a 642658 SCXA scleraxis bHLH transcription factor 642658 SCXB scleraxis bHLH transcription factor 6887 TAL2 TAL bHLH transcription factor 2 6938 TCF12 transcription factor 12 6939 TCF15 transcription factor 15 6943 TCF21 transcription factor 21 150921 TCF23 transcription factor 23 100129654 TCF24 transcription factor 24 83439 TCF3 transcription factor 7 like 1 6934 TCF4 transcription factor 7 like 2 7291 TWIST1 twist family bHLH transcription factor 1 117581 TWIST2 twist family bHLH transcription factor 2

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 1.54e-01 8.86e-28 GO E-box binding molecular_function 1.49e-01 7.78e-61 GO protein dimerization activity molecular_function 8.92e-02 2.13e-09 GO neuron fate commitment biological_process 7.59e-02 6.12e-13 GO bHLH transcription factor binding molecular_function 4.96e-02 1.95e-14 GO somitogenesis biological_process 2.63e-02 2.28e-10 Reactome CDO in myogenesis Developmental Biology 2.46e-02 2.28e-10 Reactome Myogenesis Developmental Biology 2.12e-02 4.67e-04 GO embryonic brain development biological_process 1.22e-02 1.48e-07 GO negative regulation of osteoblast differentiation biological_process 1.03e-02 1.34e-05 GO neuroblast proliferation biological_process 9.97e-03 6.12e-11 GO positive regulation of neuron differentiation biological_process 7.65e-03 6.22e-15 GO RNA polymerase II transcription factor complex cellular_component 2.48e-03 3.26e-07 GO neuron development 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 cell fate commitment 0.00e+00 0.00e+00 transcription factor complex 0.00e+00 0.00e+00 RNA polymerase II transcription factor complex 0.00e+00 0.00e+00 nuclear transcription factor complex 0.00e+00 0.00e+00 transcription regulatory region DNA binding 0.00e+00 0.00e+00 regulatory region DNA binding 0.00e+00 0.00e+00 E-box binding 0.00e+00 0.00e+00 double-stranded DNA binding 0.00e+00 0.00e+00 RNA polymerase II regulatory region sequence-specific DNA binding 0.00e+00 0.00e+00 transcription regulatory region sequence-specific DNA binding 0.00e+00 0.00e+00 RNA polymerase II transcription factor activity, sequence-specific DNA binding 0.00e+00 0.00e+00 RNA polymerase II regulatory region DNA binding 8.05e-11 6.74e-08 transcription from RNA polymerase II promoter 1.96e-09 1.41e-06 negative regulation of transcription from RNA polymerase II promoter 1.57e-08 6.97e-06 bHLH transcription factor binding 2.77e-08 1.70e-05 muscle organ development 4.09e-08 1.67e-05 transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding 4.91e-08 2.91e-05 neuron fate commitment 1.43e-07 5.37e-05 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding 2.18e-07 1.16e-04 positive regulation of cell development

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 MYOGENESIS 5.12e-10 1.74e-07 DEVELOPMENTAL BIOLOGY 1.48e-09 3.54e-07 MYOGENESIS 3.55e-04 4.76e-02 REGULATION OF BETA CELL DEVELOPMENT 2.60e-03 2.34e-01 REGULATION OF BETA CELL DEVELOPMENT

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 8.70e-06 4.26e-02 abnormal sternum ossification 1.81e-05 7.03e-02 abnormal glutaminergic neuron morphology 1.15e-04 2.48e-01 absent cerebellar lobules 1.25e-04 2.61e-01 rib bifurcation 2.08e-04 3.57e-01 abnormal myotome development 2.46e-04 3.97e-01 abnormal neuron differentiation 2.70e-04 4.21e-01 small cerebellum 3.28e-04 4.72e-01 abnormal cerebellum posterior vermis morphology 3.46e-04 4.87e-01 abnormal rib morphology 3.74e-04 5.13e-01 decreased pro-B cell number 4.42e-04 5.65e-01 abnormal neuronal precursor proliferation 4.51e-04 5.70e-01 absent myotome 4.72e-04 5.88e-01 abnormal suckling behavior 5.07e-04 6.09e-01 abnormal parasympathetic ganglion morphology 5.59e-04 6.48e-01 abnormal extraocular muscle morphology 7.42e-04 7.61e-01 abnormal paraxial mesoderm morphology 8.03e-04 7.93e-01 abnormal spinal cord interneuron morphology 9.08e-04 8.52e-01 decreased superior colliculus size 9.84e-04 8.94e-01 abnormal retinal cone bipolar cell morphology 1.13e-03 9.65e-01 abnormal cervical vertebrae morphology

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

²FDR corrected p-value (Benjamini-Hochberg)