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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod68

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod68 Module size 36 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 1952 CELSR2 cadherin EGF LAG seven-pass G-type receptor 2 22943 DKK1 dickkopf WNT signaling pathway inhibitor 1 8321 FZD1 frizzled class receptor 1 2535 FZD2 frizzled class receptor 2 8326 FZD3 frizzled class receptor 9 8322 FZD4 frizzled class receptor 4 7855 FZD5 frizzled class receptor 5 8323 FZD6 frizzled class receptor 6 8324 FZD7 frizzled class receptor 7 8325 FZD8 frizzled class receptor 8 4041 LRP5 LDL receptor related protein 5 4040 LRP6 LDL receptor related protein 6 6259 RYK receptor-like tyrosine kinase 6422 SFRP1 secreted frizzled related protein 1 6423 SFRP2 secreted frizzled related protein 2 6424 SFRP4 secreted frizzled related protein 4 6425 SFRP5 secreted frizzled related protein 5 11197 WIF1 WNT inhibitory factor 1 79971 WLS wntless Wnt ligand secretion mediator 80326 WNT10A Wnt family member 10A 7481 WNT11 Wnt family member 11 51384 WNT16 Wnt family member 16 7472 WNT2 Wnt family member 2 7482 WNT2B Wnt family member 2B 7473 WNT3 Wnt family member 3 89780 WNT3A Wnt family member 3A 54361 WNT4 Wnt family member 4 7474 WNT5A Wnt family member 5A 81029 WNT5B Wnt family member 5B 7475 WNT6 Wnt family member 6 7476 WNT7A Wnt family member 7A 7477 WNT7B Wnt family member 7B 7478 WNT8A Wnt family member 8A 7479 WNT8B Wnt family member 8B 7483 WNT9A Wnt family member 9A 7484 WNT9B Wnt family member 9B

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 3.77e-01 1.65e-45 Reactome WNT ligand biogenesis and trafficking Signal Transduction 2.17e-01 7.63e-19 Reactome RNF mutants show enhanced WNT signaling and proliferation Disease 2.07e-01 1.23e-24 Reactome Negative regulation of TCF-dependent signaling by WNT ligand antagonists Signal Transduction 1.91e-01 5.42e-34 GO Wnt-activated receptor activity molecular_function 1.85e-01 3.71e-37 GO non-canonical Wnt signaling pathway biological_process 1.14e-01 7.08e-52 GO frizzled binding molecular_function 5.37e-02 4.87e-38 GO Wnt-protein binding molecular_function 4.02e-02 5.66e-10 GO midbrain dopaminergic neuron differentiation biological_process 2.54e-02 2.98e-35 GO cell fate commitment biological_process 2.30e-02 2.61e-48 GO neuron differentiation biological_process 1.60e-02 1.04e-47 Reactome Class B/2 (Secretin family receptors) Signal Transduction 6.04e-03 8.49e-29 GO receptor ligand activity molecular_function 5.73e-03 3.76e-62 GO canonical 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 0e+00 0e+00 Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation 0e+00 0e+00 Wnt signaling pathway 0e+00 0e+00 canonical Wnt signaling pathway 0e+00 0e+00 Wnt signaling pathway, planar cell polarity pathway 0e+00 0e+00 midbrain dopaminergic neuron differentiation 0e+00 0e+00 regulation of organ morphogenesis 0e+00 0e+00 non-canonical Wnt signaling pathway 0e+00 0e+00 response to retinoic acid 0e+00 0e+00 cellular response to retinoic acid 0e+00 0e+00 regulation of canonical Wnt signaling pathway 0e+00 0e+00 regulation of Wnt signaling pathway 0e+00 0e+00 embryonic morphogenesis 0e+00 0e+00 cell fate commitment 0e+00 0e+00 tissue morphogenesis 0e+00 0e+00 extracellular matrix 0e+00 0e+00 proteinaceous extracellular matrix 0e+00 0e+00 G-protein coupled receptor binding 0e+00 0e+00 frizzled binding 0e+00 0e+00 Wnt-activated receptor activity 0e+00 0e+00 Wnt-protein binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 CLASS B 2 SECRETIN FAMILY RECEPTORS 0e+00 0e+00 GPCR LIGAND BINDING 0e+00 0e+00 CLASS B 2 SECRETIN FAMILY RECEPTORS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.59e-05 6.46e-02 abnormal hindlimb morphology 8.64e-05 2.07e-01 delayed kidney development 1.87e-04 3.34e-01 cleft upper lip 3.45e-04 4.86e-01 sirenomelia 3.46e-04 4.87e-01 abnormal Mullerian duct morphology 5.06e-04 6.09e-01 vestigial tail 7.26e-04 7.53e-01 abnormal caudal vertebrae morphology 8.27e-04 8.07e-01 abnormal limb morphology 9.84e-04 8.94e-01 abnormal tail bud morphology 1.44e-03 1.00e+00 abnormal telencephalon morphology 2.23e-03 1.00e+00 short ulna 2.61e-03 1.00e+00 pulmonary hypoplasia 2.79e-03 1.00e+00 abnormal rostral-caudal axis patterning 3.42e-03 1.00e+00 abnormal forelimb morphology 3.67e-03 1.00e+00 syndactyly 3.94e-03 1.00e+00 cleft palate 4.15e-03 1.00e+00 abnormal triploblastic development 4.72e-03 1.00e+00 abnormal long bone diaphysis morphology 5.75e-03 1.00e+00 abnormal retinal vasculature morphology 6.35e-03 1.00e+00 short fibula

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

²FDR corrected p-value (Benjamini-Hochberg)