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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod87

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod87 Module size 47 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 285 ANGPT2 angiopoietin 2 51378 ANGPT4 angiopoietin 4 1435 CSF1 colony stimulating factor 1 2246 FGF1 fibroblast growth factor 1 2255 FGF10 fibroblast growth factor 10 2256 FGF11 fibroblast growth factor 11 2257 FGF12 fibroblast growth factor 12 2258 FGF13 fibroblast growth factor 13 2259 FGF14 fibroblast growth factor 14 8823 FGF16 fibroblast growth factor 16 8822 FGF17 fibroblast growth factor 17 8817 FGF18 fibroblast growth factor 18 9965 FGF19 fibroblast growth factor 19 2258 FGF2 fibroblast growth factor 13 26281 FGF20 fibroblast growth factor 20 26291 FGF21 fibroblast growth factor 21 27006 FGF22 fibroblast growth factor 22 8074 FGF23 fibroblast growth factor 23 2248 FGF3 fibroblast growth factor 3 2249 FGF4 fibroblast growth factor 4 2250 FGF5 fibroblast growth factor 5 2251 FGF6 fibroblast growth factor 6 2252 FGF7 fibroblast growth factor 7 2253 FGF8 fibroblast growth factor 8 2254 FGF9 fibroblast growth factor 9 9982 FGFBP1 fibroblast growth factor binding protein 1 2260 FGFR1 fibroblast growth factor receptor 1 2263 FGFR2 fibroblast growth factor receptor 2 2261 FGFR3 fibroblast growth factor receptor 3 2264 FGFR4 fibroblast growth factor receptor 4 2321 FLT1 fms related tyrosine kinase 1 2324 FLT4 fms related tyrosine kinase 4 2734 GLG1 golgi glycoprotein 1 79977 GRHL2 grainyhead like transcription factor 2 57822 GRHL3 grainyhead like transcription factor 3 3791 KDR kinase insert domain receptor 152831 KLB klotho beta 197021 LCTL lactase like 9348 NDST3 N-deacetylase and N-sulfotransferase 3 64579 NDST4 N-deacetylase and N-sulfotransferase 4 56034 PDGFC platelet derived growth factor C 80310 PDGFD platelet derived growth factor D 5156 PDGFRA platelet derived growth factor receptor alpha 5228 PGF placental growth factor 29842 TFCP2L1 transcription factor CP2 like 1 79652 TMEM204 transmembrane protein 204 7342 UBP1 upstream binding protein 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 3.29e-01 1.92e-08 Reactome betaKlotho-mediated ligand binding Signal Transduction 2.66e-01 1.71e-09 GO vascular endothelial growth factor-activated receptor activity molecular_function 2.43e-01 9.97e-46 Reactome Activated point mutants of FGFR2 Disease 2.38e-01 3.30e-46 Reactome FGFR2 ligand binding and activation Signal Transduction 2.10e-01 2.46e-10 GO fibroblast growth factor-activated receptor activity molecular_function 1.88e-01 2.74e-03 Reactome t(4;14) translocations of FGFR3 Disease 1.64e-01 2.74e-03 Reactome Signaling by FGFR1 amplification mutants Disease 1.56e-01 1.54e-37 Reactome FGFR4 ligand binding and activation Signal Transduction 1.05e-01 4.08e-38 GO fibroblast growth factor receptor binding molecular_function 1.03e-01 1.79e-44 Reactome Phospholipase C-mediated cascade; FGFR2 Signal Transduction 9.57e-02 3.42e-09 Reactome VEGF ligand-receptor interactions Signal Transduction 9.56e-02 3.42e-09 Reactome VEGF binds to VEGFR leading to receptor dimerization Signal Transduction 2.94e-02 3.01e-16 Reactome FGFR1b ligand binding and activation Signal Transduction 2.45e-02 1.71e-13 GO fibroblast growth factor binding molecular_function 2.21e-02 7.90e-41 GO growth factor activity molecular_function 1.53e-02 2.34e-47 Reactome PI3K Cascade Signal Transduction 1.42e-02 1.84e-35 Reactome FGFR1 ligand binding and activation Signal Transduction 1.34e-02 3.81e-32 Reactome Signaling by activated point mutants of FGFR3 Disease 9.11e-03 8.54e-06 GO platelet-derived growth factor receptor binding molecular_function 5.24e-03 8.75e-47 GO 1-phosphatidylinositol-3-kinase activity molecular_function 4.25e-03 3.81e-32 Reactome FGFR3 mutant receptor activation Disease 2.11e-03 1.26e-44 GO phosphatidylinositol-4,5-bisphosphate 3-kinase activity molecular_function 4.81e-04 1.26e-44 Reactome Constitutive Signaling by Aberrant PI3K in Cancer Disease 1.56e-04 5.61e-04 GO activation of transmembrane receptor protein tyrosine kinase activity 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 signal transduction by protein phosphorylation 0e+00 0e+00 peptidyl-tyrosine phosphorylation 0e+00 0e+00 response to growth factor 0e+00 0e+00 regulation of phosphatidylinositol 3-kinase signaling 0e+00 0e+00 phosphatidylinositol-3-phosphate biosynthetic process 0e+00 0e+00 fibroblast growth factor receptor signaling pathway 0e+00 0e+00 phosphatidylinositol phosphorylation 0e+00 0e+00 phosphatidylinositol biosynthetic process 0e+00 0e+00 inositol lipid-mediated signaling 0e+00 0e+00 lipid phosphorylation 0e+00 0e+00 positive regulation of cell division 0e+00 0e+00 response to fibroblast growth factor 0e+00 0e+00 phospholipid biosynthetic process 0e+00 0e+00 cellular response to fibroblast growth factor stimulus 0e+00 0e+00 transmembrane receptor protein tyrosine kinase signaling pathway 0e+00 0e+00 phosphatidylinositol metabolic process 0e+00 0e+00 enzyme linked receptor protein signaling pathway 0e+00 0e+00 phosphatidylinositol-mediated signaling 0e+00 0e+00 cellular response to growth factor stimulus 0e+00 0e+00 glycerophospholipid biosynthetic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 SIGNALING BY FGFR IN DISEASE 0e+00 0e+00 NEGATIVE REGULATION OF FGFR SIGNALING 0e+00 0e+00 SIGNALING BY INSULIN RECEPTOR 0e+00 0e+00 FGFR LIGAND BINDING AND ACTIVATION 0e+00 0e+00 SIGNALING BY FGFR MUTANTS 0e+00 0e+00 ACTIVATED POINT MUTANTS OF FGFR2 0e+00 0e+00 FGFR1 LIGAND BINDING AND ACTIVATION 0e+00 0e+00 SHC MEDIATED CASCADE 0e+00 0e+00 PI 3K CASCADE 0e+00 0e+00 INSULIN RECEPTOR SIGNALLING CASCADE 0e+00 0e+00 DOWNSTREAM SIGNALING OF ACTIVATED FGFR 0e+00 0e+00 PHOSPHOLIPASE C MEDIATED CASCADE 0e+00 0e+00 FRS2 MEDIATED CASCADE 0e+00 0e+00 PI3K CASCADE 0e+00 0e+00 SIGNALING BY FGFR 0e+00 0e+00 FGFR4 LIGAND BINDING AND ACTIVATION 0e+00 0e+00 SIGNALING BY ACTIVATED POINT MUTANTS OF FGFR1 0e+00 0e+00 FGFR2C LIGAND BINDING AND ACTIVATION 0e+00 0e+00 SIGNALING BY FGFR1 MUTANTS 0e+00 0e+00 SIGNALING BY FGFR3 MUTANTS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.26e-05 1.08e-01 long incisors 3.31e-05 1.09e-01 abnormal synaptic vesicle clustering 4.67e-05 1.36e-01 absent limb buds 1.74e-04 3.22e-01 ocular hypertelorism 1.99e-04 3.48e-01 synostosis 2.79e-04 4.32e-01 enlarged lymphatic vessel 2.82e-04 4.35e-01 increased long bone epiphyseal plate size 2.98e-04 4.47e-01 abnormal coronal suture morphology 5.66e-04 6.55e-01 translucent skin 6.50e-04 7.06e-01 decreased palatal length 6.82e-04 7.26e-01 abnormal cochlea morphology 7.30e-04 7.55e-01 tongue ankylosis 7.53e-04 7.64e-01 cleft secondary palate 9.71e-04 8.90e-01 increased width of hypertrophic chondrocyte zone 1.01e-03 9.05e-01 abnormal periderm development 1.01e-03 9.05e-01 abnormal mammary placode morphology 1.01e-03 9.05e-01 absent forelimb 1.01e-03 9.05e-01 absent rectum 1.01e-03 9.05e-01 absent pulmonary artery 1.01e-03 9.05e-01 absent pulmonary vein

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

²FDR corrected p-value (Benjamini-Hochberg)