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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod309

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod309 Module size 66 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 60468 BACH2 BTB domain and CNC homolog 2 440603 BCL2L15 BCL2 like 15 54976 C20orf27 chromosome 20 open reading frame 27 23466 CBX6 chromobox 6 339965 CCDC158 coiled-coil domain containing 158 286464 CXorf30 cilia and flagella associated protein 47 340578 DCAF12L2 DDB1 and CUL4 associated factor 12 like 2 1746 DLX2 distal-less homeobox 2 1749 DLX5 distal-less homeobox 5 1760 DMPK DM1 protein kinase 9214 FAIM3 Fc fragment of IgM receptor 158297 FAM154A stabilizer of axonemal microtubules 1 170384 FUT11 fucosyltransferase 11 11036 GTF2A1L general transcription factor IIA subunit 1 like 55363 HEMGN hemogen 3087 HHEX hematopoietically expressed homeobox 22993 HMGXB3 HMG-box containing 3 3198 HOXA1 homeobox A1 3203 HOXA6 homeobox A6 3204 HOXA7 homeobox A7 3205 HOXA9 homeobox A9 147920 IGFL2 IGF like family member 2 57117 INTS12 integrator complex subunit 12 79191 IRX3 iroquois homeobox 3 50805 IRX4 iroquois homeobox 4 79190 IRX6 iroquois homeobox 6 90011 KIR3DX1 killer cell immunoglobulin like receptor, three Ig domains X1 4094 MAF MAF bZIP transcription factor 9935 MAFB MAF bZIP transcription factor B 4223 MEOX2 mesenchyme homeobox 2 283078 MKX mohawk homeobox 345222 MSANTD1 Myb/SANT DNA binding domain containing 1 22823 MTF2 metal response element binding transcription factor 2 4779 NFE2L1 nuclear factor, erythroid 2 like 1 9603 NFE2L3 nuclear factor, erythroid 2 like 3 159296 NKX2-3 NK2 homeobox 3 4863 NPAT nuclear protein, coactivator of histone transcription 2494 NR5A2 nuclear receptor subfamily 5 group A member 2 51667 NUB1 negative regulator of ubiquitin like proteins 1 29948 OSGIN1 oxidative stress induced growth inhibitor 1 139793 PAGE3 PAGE family member 3 25891 PAMR1 peptidase domain containing associated with muscle regeneration 1 5075 PAX1 paired box 1 8050 PDX1 pyruvate dehydrogenase complex component X 23042 PDXDC1 pyridoxal dependent decarboxylase domain containing 1 5252 PHF1 PHD finger protein 1 26147 PHF19 PHD finger protein 19 63876 PKNOX2 PBX/knotted 1 homeobox 2 100101267 POM121C POM121 transmembrane nucleoporin C 5450 POU2AF1 POU class 2 associating factor 1 5451 POU2F1 POU class 2 homeobox 1 5629 PROX1 prospero homeobox 1 284338 PRR19 proline rich 19 285282 RABL3 RAB, member of RAS oncogene family like 3 57529 RGAG1 retrotransposon Gag like 9 22955 SCMH1 Scm polycomb group protein homolog 1 6414 SEPP1 selenoprotein P 6665 SOX15 SRY-box 15 30812 SOX8 SRY-box 8 84654 SPZ1 spermatogenic leucine zipper 1 219736 STOX1 storkhead box 1 219899 TBCEL tubulin folding cofactor E like 60436 TGIF2 TGFB induced factor homeobox 2 375337 TOPAZ1 testis and ovary specific PAZ domain containing 1 128553 TSHZ2 teashirt zinc finger homeobox 2 8433 UTF1 undifferentiated embryonic cell transcription factor 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 1.09e-01 1.09e-04 Reactome Regulation of gene expression in early pancreatic precursor cells Developmental Biology 3.71e-02 1.52e-05 GO HMG box domain binding molecular_function 3.48e-02 1.52e-05 GO ESC/E(Z) complex cellular_component 1.63e-02 2.85e-05 GO RNA polymerase II core promoter sequence-specific DNA binding molecular_function 7.11e-03 4.23e-05 GO nucleosome binding molecular_function 2.31e-03 2.05e-07 GO RNA polymerase II distal enhancer sequence-specific DNA binding molecular_function

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 1.48e-09 7.64e-07 RNA polymerase II transcription factor activity, sequence-specific DNA binding 1.61e-09 1.17e-06 transcription from RNA polymerase II promoter 2.48e-08 1.06e-05 transcription regulatory region sequence-specific DNA binding 4.77e-08 1.93e-05 RNA polymerase II regulatory region sequence-specific DNA binding 4.92e-08 1.98e-05 RNA polymerase II regulatory region DNA binding 1.24e-07 4.70e-05 double-stranded DNA binding 2.28e-07 8.21e-05 transcription regulatory region DNA binding 2.30e-07 8.28e-05 regulatory region DNA binding 2.34e-07 1.24e-04 pattern specification process 3.30e-07 1.71e-04 segment specification 1.36e-06 6.30e-04 negative regulation of transcription from RNA polymerase II promoter 1.39e-06 6.43e-04 positive regulation of histone H3-K27 methylation 2.65e-06 7.20e-04 PcG protein complex 5.43e-06 2.23e-03 regulation of histone H3-K27 methylation 5.96e-06 2.42e-03 embryonic morphogenesis 6.70e-06 1.69e-03 ESC/E(Z) complex 1.14e-05 2.94e-03 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding 3.51e-05 8.23e-03 transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding 4.75e-05 1.53e-02 segmentation 5.00e-05 1.60e-02 negative regulation of histone H3-K27 methylation

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.43e-04 1.76e-02 REGULATION OF BETA CELL DEVELOPMENT 2.55e-04 3.55e-02 REGULATION OF BETA CELL DEVELOPMENT 5.11e-03 4.18e-01 NUCLEAR RECEPTOR TRANSCRIPTION PATHWAY 6.46e-03 5.11e-01 SMAD2 SMAD3 SMAD4 HETEROTRIMER REGULATES TRANSCRIPTION 9.66e-03 7.14e-01 DOWNREGULATION OF SMAD2 3 SMAD4 TRANSCRIPTIONAL ACTIVITY 9.69e-03 7.15e-01 TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER 1.15e-02 8.90e-01 SMAD2 SMAD3 SMAD4 HETEROTRIMER REGULATES TRANSCRIPTION 1.27e-02 9.62e-01 DOWNREGULATION OF SMAD2 3 SMAD4 TRANSCRIPTIONAL ACTIVITY 1.47e-02 1.00e+00 REGULATION OF GENE EXPRESSION IN BETA CELLS 1.73e-02 1.00e+00 TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER 1.89e-02 1.00e+00 REGULATION OF GENE EXPRESSION IN BETA CELLS 2.12e-02 1.00e+00 SIGNALING BY TGF BETA RECEPTOR COMPLEX 2.20e-02 1.00e+00 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 3 PROMOTER 2.55e-02 1.00e+00 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 3 PROMOTER 3.12e-02 1.00e+00 RNA POL III TRANSCRIPTION 3.19e-02 1.00e+00 SIGNALING BY TGF BETA RECEPTOR COMPLEX 3.25e-02 1.00e+00 NUCLEAR RECEPTOR TRANSCRIPTION PATHWAY 3.95e-02 1.00e+00 DEVELOPMENTAL BIOLOGY 4.73e-02 1.00e+00 RNA POL III TRANSCRIPTION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.79e-05 9.83e-02 absent endolymphatic duct 2.25e-04 3.75e-01 increased rib number 4.10e-04 5.37e-01 abnormal hyoid bone greater horn morphology 4.55e-04 5.73e-01 ectopic cartilage 5.96e-04 6.73e-01 wavy tail 9.76e-04 8.93e-01 absent superior semicircular canal 1.42e-03 1.00e+00 abnormal vestibular saccular macula morphology 1.71e-03 1.00e+00 abnormal liver development 1.99e-03 1.00e+00 abnormal semicircular canal morphology 2.19e-03 1.00e+00 abnormal utricular macula morphology 2.26e-03 1.00e+00 abnormal pterygoid bone morphology 2.45e-03 1.00e+00 absent palatine bone horizontal plate 2.90e-03 1.00e+00 abnormal rhombomere morphology 3.07e-03 1.00e+00 absent posterior semicircular canal 3.11e-03 1.00e+00 absent semicircular canals 3.69e-03 1.00e+00 abnormal anterior visceral endoderm morphology 4.10e-03 1.00e+00 abnormal otic capsule morphology 4.13e-03 1.00e+00 abnormal membranous labyrinth morphology 4.72e-03 1.00e+00 absent stapes 5.41e-03 1.00e+00 small pancreas

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

²FDR corrected p-value (Benjamini-Hochberg)