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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod308

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod308 Module size 41 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 170689 ADAMTS15 ADAM metallopeptidase with thrombospondin type 1 motif 15 213 ALB albumin 200576 CFD phosphoinositide kinase, FYVE-type zinc finger containing 303300 CLU clustered mitochondria homolog 2162 F13A1 coagulation factor XIII A chain 2153 F5 coagulation factor V 2277 FIGF vascular endothelial growth factor D 2621 GAS6 growth arrest specific 6 3084 HRG neuregulin 1 3479 IGF1 insulin like growth factor 1 3481 IGF2 insulin like growth factor 2 3484 IGFBP1 insulin like growth factor binding protein 1 3486 IGFBP3 insulin like growth factor binding protein 3 3487 IGFBP4 insulin like growth factor binding protein 4 3488 IGFBP5 insulin like growth factor binding protein 5 3489 IGFBP6 insulin like growth factor binding protein 6 7044 LEFTY2 left-right determination factor 2 4054 LTBP3 latent transforming growth factor beta binding protein 3 22915 MMRN1 multimerin 1 5069 PAPPA pappalysin 1 60676 PAPPA2 pappalysin 2 5196 PF4 platelet factor 4 5553 PRG2 proteoglycan 2, pro eosinophil major basic protein 5627 PROS1 protein S 5265 SERPINA1 serpin family A member 1 5054 SERPINE1 serpin family E member 1 5345 SERPINF2 serpin family F member 2 710 SERPING1 serpin family G member 1 6678 SPARC secreted protein acidic and cysteine rich 5552 SRGN serglycin 7042 TGFB2 transforming growth factor beta 2 7043 TGFB3 transforming growth factor beta 3 7056 THBD thrombomodulin 7076 TIMP1 TIMP metallopeptidase inhibitor 1 7114 TMSB4X thymosin beta 4 X-linked 7148 TNXB tenascin XB 7422 VEGFA vascular endothelial growth factor A 7423 VEGFB vascular endothelial growth factor B 7424 VEGFC vascular endothelial growth factor C 7450 VWF von Willebrand factor 8839 WISP2 WNT1 inducible signaling pathway protein 2

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 3.54e-01 2.94e-12 GO insulin-like growth factor II binding molecular_function 3.02e-01 2.42e-58 GO platelet alpha granule lumen cellular_component 9.16e-02 2.33e-03 Reactome Defective SLCO1B1 causes hyperbilirubinemia, Rotor type (HBLRR) Disease 7.62e-02 5.24e-09 GO negative regulation of fibrinolysis biological_process 7.30e-02 2.33e-03 Reactome Defective SLCO1B3 causes hyperbilirubinemia, Rotor type (HBLRR) Disease 4.25e-02 1.78e-08 GO positive regulation of insulin-like growth factor receptor signaling pathway biological_process 4.22e-02 4.14e-11 GO insulin-like growth factor I binding molecular_function 1.91e-02 6.50e-07 Reactome VEGF binds to VEGFR leading to receptor dimerization Signal Transduction 1.85e-02 6.50e-07 Reactome VEGF ligand-receptor interactions Signal Transduction 5.66e-03 8.65e-21 Reactome Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) Metabolism of proteins

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 exocytosis 0.00e+00 0.00e+00 regulated exocytosis 0.00e+00 0.00e+00 platelet degranulation 0.00e+00 0.00e+00 platelet alpha granule lumen 0.00e+00 0.00e+00 platelet alpha granule 0.00e+00 0.00e+00 secretory granule 0.00e+00 0.00e+00 cytoplasmic vesicle lumen 0.00e+00 0.00e+00 secretory granule lumen 3.79e-11 3.28e-08 wound healing 2.31e-10 1.35e-07 insulin-like growth factor II binding 3.02e-10 1.46e-07 extracellular matrix 3.84e-10 2.19e-07 insulin-like growth factor binding 1.70e-09 8.69e-07 insulin-like growth factor I binding 1.88e-09 1.35e-06 response to wounding 4.41e-09 2.12e-06 growth factor activity 8.97e-09 5.87e-06 regulation of insulin-like growth factor receptor signaling pathway 1.50e-08 6.68e-06 growth factor binding 5.43e-08 1.95e-05 insulin-like growth factor binding protein complex 5.43e-08 1.95e-05 insulin-like growth factor ternary complex 1.33e-07 7.36e-05 regulation of body fluid levels

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 INSULIN LIKE GROWTH FACTOR IGF ACTIVITY BY INSULIN LIKE GROWTH FACTOR BINDING PROTEINS IGFBPS 0.00e+00 0.00e+00 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2 0.00e+00 0.00e+00 PLATELET ACTIVATION SIGNALING AND AGGREGATION 0.00e+00 0.00e+00 REGULATION OF INSULIN LIKE GROWTH FACTOR IGF ACTIVITY BY INSULIN LIKE GROWTH FACTOR BINDING PROTEINS IGFBPS 0.00e+00 0.00e+00 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2 0.00e+00 0.00e+00 PLATELET ACTIVATION SIGNALING AND AGGREGATION 1.05e-09 3.46e-07 FORMATION OF FIBRIN CLOT CLOTTING CASCADE 1.35e-09 3.24e-07 FORMATION OF FIBRIN CLOT CLOTTING CASCADE 2.11e-08 4.46e-06 COMMON PATHWAY 5.28e-08 1.41e-05 COMMON PATHWAY 8.96e-08 1.75e-05 VEGF LIGAND RECEPTOR INTERACTIONS 1.26e-06 2.15e-04 DIABETES PATHWAYS 1.80e-06 3.87e-04 VEGF LIGAND RECEPTOR INTERACTIONS 3.05e-06 6.33e-04 DIABETES PATHWAYS 5.14e-03 4.68e-01 INTRINSIC PATHWAY 7.42e-03 5.74e-01 INTRINSIC PATHWAY 1.05e-02 7.62e-01 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 1.56e-02 1.00e+00 COMPLEMENT CASCADE 2.13e-02 1.00e+00 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 2.36e-02 1.00e+00 COMPLEMENT CASCADE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 9.98e-09 2.54e-04 abnormal blood coagulation 4.24e-05 1.29e-01 increased vascular permeability 2.00e-04 3.50e-01 thrombosis 2.71e-04 4.22e-01 increased sensitivity to induced morbidity/mortality 5.77e-04 6.61e-01 persistent right dorsal aorta 1.39e-03 1.00e+00 abnormal enterocyte apoptosis 1.48e-03 1.00e+00 decreased birth weight 2.10e-03 1.00e+00 hemothorax 2.86e-03 1.00e+00 aortic aneurysm 3.05e-03 1.00e+00 abnormal heart morphology 3.08e-03 1.00e+00 abnormal thoracic cage shape 3.41e-03 1.00e+00 abnormal mandible morphology 3.51e-03 1.00e+00 dilated respiratory conducting tubes 4.54e-03 1.00e+00 short mandible 4.63e-03 1.00e+00 enhanced wound healing 4.71e-03 1.00e+00 respiratory system inflammation 4.74e-03 1.00e+00 abnormal heart septum morphology 6.04e-03 1.00e+00 abnormal small intestinal villus morphology 6.17e-03 1.00e+00 proportional dwarf 6.20e-03 1.00e+00 abnormal impulse conducting system conduction

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

²FDR corrected p-value (Benjamini-Hochberg)