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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod3

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod3 Module size 41 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 23452 ANGPTL2 angiopoietin like 2 253935 ANGPTL5 angiopoietin like 5 430 ASCL2 achaete-scute family bHLH transcription factor 2 8538 BARX2 BARX homeobox 2 168620 BHLHA15 basic helix-loop-helix family member a15 9256 BZRAP1 TSPO associated protein 1 89927 C16orf45 chromosome 16 open reading frame 45 441150 C6orf226 chromosome 6 open reading frame 226 863 CBFA2T3 CBFA2/RUNX1 translocation partner 3 255101 CCDC108 cilia and flagella associated protein 65 23582 CCNDBP1 cyclin D1 binding protein 1 64100 ELSPBP1 epididymal sperm binding protein 1 9747 FAM115A TRPM8 channel associated factor 1 2208 FCER2 Fc fragment of IgE receptor II 388698 FLG2 filaggrin family member 2 90167 FRMD7 FERM domain containing 7 6928 HNF1B HNF1 homeobox B 3397 ID1 inhibitor of DNA binding 1, HLH protein 3428 IFI16 interferon gamma inducible protein 16 3642 INSM1 INSM transcriptional repressor 1 84684 INSM2 INSM transcriptional repressor 2 81606 LBH limb bud and heart development 10219 MAFA killer cell lectin like receptor G1 4188 MDFI MyoD family inhibitor 29969 MDFIC MyoD family inhibitor domain containing 4654 MYOD1 myogenic differentiation 1 4760 NEUROD1 neuronal differentiation 1 7080 NKX2-1 NK2 homeobox 1 4821 NKX2-2 NK2 homeobox 2 4825 NKX6-1 NK6 homeobox 1 126206 NLRP5 NLR family pyrin domain containing 5 3175 ONECUT1 one cut homeobox 1 390874 ONECUT3 one cut homeobox 3 160065 PATE1 prostate and testis expressed 1 5375 PMP2 peripheral myelin protein 2 112476 PRRT2 proline rich transmembrane protein 2 253959 RALGAPA1 Ral GTPase activating protein catalytic alpha subunit 1 862 RUNX1T1 RUNX1 translocation partner 1 6659 SOX4 SRY-box 4 23334 SZT2 SZT2, KICSTOR complex subunit 144404 TMEM120B transmembrane protein 120B

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 4.19e-01 2.58e-08 Reactome Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells Developmental Biology 2.12e-01 1.29e-07 Reactome Regulation of gene expression in early pancreatic precursor cells Developmental Biology 1.41e-01 2.14e-05 Reactome Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells Developmental Biology 3.10e-02 2.29e-14 Reactome Regulation of beta-cell development Developmental Biology

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 2.03e-08 1.27e-05 endocrine pancreas development 2.92e-08 1.23e-05 RNA polymerase II transcription factor activity, sequence-specific DNA binding 3.54e-07 1.23e-04 transcription regulatory region DNA binding 3.56e-07 1.23e-04 regulatory region DNA binding 5.12e-07 2.57e-04 pancreas development 5.88e-07 1.95e-04 transcription regulatory region sequence-specific DNA binding 8.62e-07 2.55e-04 transcription factor complex 1.65e-06 5.04e-04 RNA polymerase II regulatory region sequence-specific DNA binding 1.70e-06 5.17e-04 RNA polymerase II regulatory region DNA binding 1.92e-06 5.77e-04 double-stranded DNA binding 2.10e-06 9.38e-04 pancreatic A cell differentiation 3.30e-06 1.42e-03 enteroendocrine cell differentiation 2.58e-05 8.99e-03 response to glucose 2.98e-05 7.10e-03 transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding 3.38e-05 7.96e-03 core promoter proximal region DNA binding 4.31e-05 1.41e-02 type B pancreatic cell development 4.54e-05 1.47e-02 cell fate commitment 5.85e-05 1.84e-02 glandular epithelial cell differentiation 6.19e-05 1.93e-02 epithelial cell differentiation 8.12e-05 2.44e-02 response to carbohydrate

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 REGULATION OF BETA CELL DEVELOPMENT 0.00e+00 0.00e+00 REGULATION OF BETA CELL DEVELOPMENT 2.28e-09 7.16e-07 DEVELOPMENTAL BIOLOGY 1.07e-08 2.34e-06 REGULATION OF GENE EXPRESSION IN BETA CELLS 2.35e-08 6.60e-06 REGULATION OF GENE EXPRESSION IN BETA CELLS 3.32e-02 1.00e+00 MYOGENESIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.42e-07 2.87e-03 decreased pancreatic beta cell number 3.89e-07 4.28e-03 decreased pancreatic alpha cell number 4.23e-06 2.56e-02 decreased pancreatic delta cell number 1.49e-04 2.94e-01 decreased insulin secretion 2.99e-04 4.47e-01 abnormal endocrine pancreas development 3.05e-04 4.52e-01 abnormal pancreas morphology 4.71e-04 5.87e-01 abnormal pancreatic islet morphology 5.45e-04 6.40e-01 abnormal pituitary gland development 7.34e-04 7.57e-01 tracheoesophageal fistula 8.99e-04 8.46e-01 absent pancreatic beta cells 9.00e-04 8.47e-01 abnormal lung epithelium morphology 1.10e-03 9.51e-01 disorganized pancreatic islets 1.13e-03 9.65e-01 increased liver adenoma incidence 1.38e-03 1.00e+00 abnormal mammary gland alveolus morphology 1.52e-03 1.00e+00 abnormal neuron specification 2.70e-03 1.00e+00 abnormal pancreatic acinar cell morphology 3.35e-03 1.00e+00 abnormal mammary gland growth during lactation 3.77e-03 1.00e+00 abnormal mesenchymal cell differentiation involved in lung development 5.62e-03 1.00e+00 increased number of pulmonary neuroendocrine bodies 5.63e-03 1.00e+00 impaired branching involved in respiratory bronchiole morphogenesis

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

²FDR corrected p-value (Benjamini-Hochberg)