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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod174

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod174 Module size 43 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 147495 APCDD1 APC down-regulated 1 56033 BARX1 BARX homeobox 1 114902 C1QTNF5 C1q and TNF related 5 9620 CELSR1 cadherin EGF LAG seven-pass G-type receptor 1 1951 CELSR3 cadherin EGF LAG seven-pass G-type receptor 3 10699 CORIN corin, serine peptidase 115908 CTHRC1 collagen triple helix repeat containing 1 80319 CXXC4 CXXC finger protein 4 1855 DVL1 dishevelled segment polarity protein 1 1856 DVL2 dishevelled segment polarity protein 2 1857 DVL3 dishevelled segment polarity protein 3 2487 FRZB frizzled related protein 80199 FUZ fuzzy planar cell polarity protein 11211 FZD10 frizzled class receptor 10 8326 FZD9 frizzled class receptor 9 27152 INTU inturned planar cell polarity protein 83999 KREMEN1 kringle containing transmembrane protein 1 79412 KREMEN2 kringle containing transmembrane protein 2 83552 MFRP membrane frizzled-related protein 4693 NDP NDP, norrin cystine knot growth factor 85407 NKD1 naked cuticle homolog 1 5076 PAX2 paired box 2 64881 PCDH20 protocadherin 20 57475 PLEKHH1 pleckstrin homology, MyTH4 and FERM domain containing H1 166336 PRICKLE2 prickle planar cell polarity protein 2 4007 PRICKLE3 prickle planar cell polarity protein 3 6002 RGS12 regulator of G protein signaling 12 6003 RGS13 regulator of G protein signaling 13 6004 RGS16 regulator of G protein signaling 16 431704 RGS21 regulator of G protein signaling 21 8490 RGS5 regulator of G protein signaling 5 85397 RGS8 regulator of G protein signaling 8 6095 ROR2 RAR related orphan receptor A 50964 SOST sclerostin 50999 TMED5 transmembrane p24 trafficking protein 5 92162 TMEM88 transmembrane protein 88 23554 TSPAN12 tetraspanin 12 81839 VANGL1 VANGL planar cell polarity protein 1 57216 VANGL2 VANGL planar cell polarity protein 2 7471 WNT1 Wnt family member 1 7480 WNT10B Wnt family member 10B 114786 XKR4 XK related 4 343702 XKR7 XK related 7

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 4.35e-01 1.26e-10 Reactome Negative regulation of TCF-dependent signaling by DVL-interacting proteins Signal Transduction 9.83e-02 2.48e-08 GO establishment of planar polarity biological_process 9.83e-02 7.89e-05 Reactome Misspliced LRP5 mutants have enhanced beta-catenin-dependent signaling Disease 7.92e-02 3.24e-18 GO Wnt signaling pathway, planar cell polarity pathway biological_process 5.70e-02 1.41e-11 GO cochlea morphogenesis biological_process 3.99e-02 3.71e-14 GO frizzled binding molecular_function 3.16e-02 2.38e-10 GO Wnt-protein binding molecular_function 1.30e-02 9.32e-06 GO negative regulation of ossification biological_process 3.77e-03 6.21e-08 GO negative regulation of signal transduction biological_process 2.25e-03 9.35e-08 GO negative regulation of Wnt signaling pathway 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 Wnt signaling pathway 0.00e+00 0.00e+00 regulation of canonical Wnt signaling pathway 0.00e+00 0.00e+00 regulation of Wnt signaling pathway 0.00e+00 0.00e+00 negative regulation of Wnt signaling pathway 0.00e+00 0.00e+00 Wnt signaling pathway, planar cell polarity pathway 0.00e+00 0.00e+00 non-canonical Wnt signaling pathway 0.00e+00 0.00e+00 frizzled binding 2.90e-11 2.53e-08 inner ear morphogenesis 1.02e-10 8.45e-08 cochlea morphogenesis 1.18e-10 9.72e-08 sensory organ development 2.84e-10 1.65e-07 Wnt-protein binding 3.38e-10 2.66e-07 ear morphogenesis 7.20e-10 5.45e-07 inner ear development 1.06e-09 7.88e-07 negative regulation of canonical Wnt signaling pathway 3.55e-09 2.45e-06 ear development 4.69e-09 3.18e-06 regulation of organ morphogenesis 8.81e-09 5.77e-06 cochlea development 1.39e-08 6.21e-06 G-protein coupled receptor binding 1.46e-08 9.31e-06 planar cell polarity pathway involved in neural tube closure 1.93e-08 1.21e-05 neural tube development

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 5.33e-05 8.85e-03 CLASS B 2 SECRETIN FAMILY RECEPTORS 1.53e-04 1.86e-02 CLASS B 2 SECRETIN FAMILY RECEPTORS 2.52e-03 2.28e-01 G ALPHA I SIGNALLING EVENTS 3.35e-03 2.92e-01 TRANSCRIPTIONAL REGULATION OF WHITE ADIPOCYTE DIFFERENTIATION 5.91e-03 5.25e-01 G ALPHA I SIGNALLING EVENTS 6.18e-03 5.44e-01 TRANSCRIPTIONAL REGULATION OF WHITE ADIPOCYTE DIFFERENTIATION 8.57e-03 7.08e-01 GPCR LIGAND BINDING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.99e-05 1.79e-01 abnormal midbrain morphology 8.18e-05 1.99e-01 abnormal orientation of cochlear hair cell stereociliary bundles 9.14e-05 2.12e-01 small floor plate 2.47e-04 3.97e-01 abnormal neural tube closure 2.48e-04 3.97e-01 absent midbrain-hindbrain boundary 3.44e-04 4.86e-01 impaired branching involved in terminal bronchiole morphogenesis 5.04e-04 6.07e-01 dilated terminal bronchiole tubes 5.36e-04 6.34e-01 short scala media 7.09e-04 7.41e-01 delayed neural tube closure 7.54e-04 7.64e-01 abnormal cranial flexure morphology 9.08e-04 8.52e-01 abnormal stria vascularis vasculature morphology 9.63e-04 8.85e-01 small lung lobe 9.83e-04 8.94e-01 abnormal metencephalon morphology 1.14e-03 9.71e-01 abnormal somite size 1.52e-03 1.00e+00 abnormal lung lobe morphology 1.73e-03 1.00e+00 craniorachischisis 1.89e-03 1.00e+00 abnormal respiratory conducting tube morphology 2.24e-03 1.00e+00 increased bone strength 2.33e-03 1.00e+00 decreased bone trabecula number 2.38e-03 1.00e+00 absent cerebellum

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

²FDR corrected p-value (Benjamini-Hochberg)