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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod189

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod189 Module size 40 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 1300 COL10A1 collagen type X alpha 1 chain 1301 COL11A1 collagen type XI alpha 1 chain 1303 COL12A1 collagen type XII alpha 1 chain 1305 COL13A1 collagen type XIII alpha 1 chain 7373 COL14A1 collagen type XIV alpha 1 chain 1306 COL15A1 collagen type XV alpha 1 chain 1307 COL16A1 collagen type XVI alpha 1 chain 1308 COL17A1 collagen type XVII alpha 1 chain 80781 COL18A1 collagen type XVIII alpha 1 chain 1310 COL19A1 collagen type XIX alpha 1 chain 1277 COL1A1 collagen type I alpha 1 chain 1278 COL1A2 collagen type I alpha 2 chain 57642 COL20A1 collagen type XX alpha 1 chain 81578 COL21A1 collagen type XXI alpha 1 chain 169044 COL22A1 collagen type XXII alpha 1 chain 91522 COL23A1 collagen type XXIII alpha 1 chain 255631 COL24A1 collagen type XXIV alpha 1 chain 84570 COL25A1 collagen type XXV alpha 1 chain 85301 COL27A1 collagen type XXVII alpha 1 chain 340267 COL28A1 collagen type XXVIII alpha 1 chain 1280 COL2A1 collagen type II alpha 1 chain 1281 COL3A1 collagen type III alpha 1 chain 1282 COL4A1 collagen type IV alpha 1 chain 1284 COL4A2 collagen type IV alpha 2 chain 1285 COL4A3 collagen type IV alpha 3 chain 1286 COL4A4 collagen type IV alpha 4 chain 1287 COL4A5 collagen type IV alpha 5 chain 1288 COL4A6 collagen type IV alpha 6 chain 1289 COL5A1 collagen type V alpha 1 chain 1290 COL5A2 collagen type V alpha 2 chain 50509 COL5A3 collagen type V alpha 3 chain 1291 COL6A1 collagen type VI alpha 1 chain 1292 COL6A2 collagen type VI alpha 2 chain 1293 COL6A3 collagen type VI alpha 3 chain 1294 COL7A1 collagen type VII alpha 1 chain 1295 COL8A1 collagen type VIII alpha 1 chain 1296 COL8A2 collagen type VIII alpha 2 chain 1297 COL9A1 collagen type IX alpha 1 chain 1298 COL9A2 collagen type IX alpha 2 chain 1299 COL9A3 collagen type IX alpha 3 chain

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 6.79e-01 4.65e-117 Reactome Collagen chain trimerization Extracellular matrix organization 6.12e-02 5.66e-104 Reactome Collagen biosynthesis and modifying enzymes Extracellular matrix organization 4.81e-02 2.78e-67 GO extracellular matrix structural constituent conferring tensile strength molecular_function 2.85e-02 1.08e-16 GO collagen type IV trimer cellular_component

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 extracellular structure organization 0.00e+00 0.00e+00 extracellular matrix organization 0.00e+00 0.00e+00 collagen catabolic process 0.00e+00 0.00e+00 multicellular organism metabolic process 0.00e+00 0.00e+00 multicellular organismal macromolecule metabolic process 0.00e+00 0.00e+00 collagen metabolic process 0.00e+00 0.00e+00 collagen fibril organization 0.00e+00 0.00e+00 endoplasmic reticulum lumen 0.00e+00 0.00e+00 basement membrane 0.00e+00 0.00e+00 collagen trimer 0.00e+00 0.00e+00 extracellular matrix 0.00e+00 0.00e+00 collagen type IV trimer 0.00e+00 0.00e+00 proteinaceous extracellular matrix 0.00e+00 0.00e+00 fibrillar collagen trimer 0.00e+00 0.00e+00 structural molecule activity 0.00e+00 0.00e+00 extracellular matrix structural constituent 0.00e+00 0.00e+00 platelet-derived growth factor binding 2.66e-12 1.82e-09 extracellular matrix structural constituent conferring tensile strength 2.24e-11 1.98e-08 collagen-activated tyrosine kinase receptor signaling pathway 6.73e-11 5.69e-08 collagen-activated signaling pathway

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 EXTRACELLULAR MATRIX ORGANIZATION 0.00e+00 0.00e+00 COLLAGEN FORMATION 0.00e+00 0.00e+00 NCAM SIGNALING FOR NEURITE OUT GROWTH 0.00e+00 0.00e+00 SIGNALING BY PDGF 0.00e+00 0.00e+00 AXON GUIDANCE 0.00e+00 0.00e+00 NCAM1 INTERACTIONS 0.00e+00 0.00e+00 EXTRACELLULAR MATRIX ORGANIZATION 0.00e+00 0.00e+00 COLLAGEN FORMATION 0.00e+00 0.00e+00 SIGNALING BY PDGF 0.00e+00 0.00e+00 AXON GUIDANCE 0.00e+00 0.00e+00 NCAM1 INTERACTIONS 0.00e+00 0.00e+00 NCAM SIGNALING FOR NEURITE OUT GROWTH 7.82e-09 2.32e-06 DEVELOPMENTAL BIOLOGY 6.60e-08 1.31e-05 INTEGRIN CELL SURFACE INTERACTIONS 1.92e-06 4.11e-04 INTEGRIN CELL SURFACE INTERACTIONS 4.01e-03 3.40e-01 PLATELET ADHESION TO EXPOSED COLLAGEN 6.02e-03 5.33e-01 PLATELET ADHESION TO EXPOSED COLLAGEN 1.06e-02 7.68e-01 GPVI MEDIATED ACTIVATION CASCADE 4.72e-02 1.00e+00 GPVI MEDIATED ACTIVATION CASCADE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.91e-06 1.43e-02 decreased tendon stiffness 3.70e-06 2.32e-02 myopathy 4.77e-06 2.84e-02 decreased skin tensile strength 5.43e-06 3.12e-02 abnormal cutaneous collagen fibril morphology 5.89e-06 3.23e-02 decreased corneal stroma thickness 1.38e-05 5.80e-02 podocyte foot process effacement 7.90e-05 1.94e-01 abnormal dermal layer morphology 1.08e-04 2.39e-01 abnormal tendon morphology 1.18e-04 2.51e-01 osteoarthritis 1.77e-04 3.24e-01 abnormal eye anterior chamber morphology 1.90e-04 3.37e-01 anterior polar cataracts 2.45e-04 3.97e-01 abnormal basement membrane morphology 2.47e-04 3.97e-01 abnormal compact bone lamellar structure 2.47e-04 3.97e-01 abnormal tendon collagen fibril morphology 2.61e-04 4.11e-01 abnormal long bone epiphyseal plate proliferative zone 2.62e-04 4.12e-01 abnormal joint morphology 2.87e-04 4.38e-01 abnormal femur morphology 3.45e-04 4.86e-01 abnormal chondrocyte morphology 3.62e-04 5.01e-01 renal glomerular synechia 3.64e-04 5.02e-01 buphthalmos

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

²FDR corrected p-value (Benjamini-Hochberg)