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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod58

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod58 Module size 33 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 176 ACAN aggrecan 100131137 BSPH1 binder of sperm protein homolog 1 1192 CLIC1 chloride intracellular channel 1 1404 HAPLN1 hyaluronan and proteoglycan link protein 1 3934 LCN2 lipocalin 2 4312 MMP1 matrix metallopeptidase 1 4319 MMP10 matrix metallopeptidase 10 4320 MMP11 matrix metallopeptidase 11 4322 MMP13 matrix metallopeptidase 13 4323 MMP14 matrix metallopeptidase 14 4324 MMP15 matrix metallopeptidase 15 4325 MMP16 matrix metallopeptidase 16 4326 MMP17 matrix metallopeptidase 17 4327 MMP19 matrix metallopeptidase 19 4313 MMP2 matrix metallopeptidase 2 8510 MMP21 matrix metallopeptidase 23B 8510 MMP23B matrix metallopeptidase 23B 64386 MMP25 matrix metallopeptidase 25 56547 MMP26 matrix metallopeptidase 26 64066 MMP27 matrix metallopeptidase 27 79148 MMP28 matrix metallopeptidase 28 4314 MMP3 matrix metallopeptidase 3 4316 MMP7 matrix metallopeptidase 7 4317 MMP8 matrix metallopeptidase 8 4318 MMP9 matrix metallopeptidase 9 4811 NID1 nidogen 1 57125 PLXDC1 plexin domain containing 1 64748 PRG4 phospholipid phosphatase related 2 8434 RECK reversion inducing cysteine rich protein with kazal motifs 7077 TIMP2 TIMP metallopeptidase inhibitor 2 7078 TIMP3 TIMP metallopeptidase inhibitor 3 7079 TIMP4 TIMP metallopeptidase inhibitor 4 7369 UMOD uromodulin

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 2.61e-01 3.51e-35 Reactome Activation of Matrix Metalloproteinases Extracellular matrix organization 1.95e-01 1.09e-33 GO collagen catabolic process biological_process 8.30e-02 2.96e-07 GO negative regulation of membrane protein ectodomain proteolysis biological_process 6.81e-02 1.17e-08 GO metalloendopeptidase inhibitor activity molecular_function 6.79e-02 1.91e-06 GO extracellular matrix structural constituent conferring compression resistance molecular_function 4.20e-03 3.30e-08 GO metalloaminopeptidase activity molecular_function

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 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 extracellular matrix disassembly 0.00e+00 0.00e+00 extracellular structure organization 0.00e+00 0.00e+00 extracellular matrix organization 0.00e+00 0.00e+00 extracellular matrix 0.00e+00 0.00e+00 proteinaceous extracellular matrix 0.00e+00 0.00e+00 calcium ion binding 0.00e+00 0.00e+00 endopeptidase activity 0.00e+00 0.00e+00 peptidase activity 0.00e+00 0.00e+00 metalloendopeptidase activity 0.00e+00 0.00e+00 metallopeptidase activity 3.26e-10 1.88e-07 serine-type endopeptidase activity 7.81e-10 4.21e-07 serine-type peptidase activity 8.64e-10 4.64e-07 serine hydrolase activity 5.71e-08 3.35e-05 endodermal cell differentiation 1.62e-07 8.83e-05 endoderm formation 4.51e-07 2.28e-04 negative regulation of metallopeptidase activity

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 DEGRADATION OF THE EXTRACELLULAR MATRIX 0.00e+00 0.00e+00 EXTRACELLULAR MATRIX ORGANIZATION 0.00e+00 0.00e+00 EXTRACELLULAR MATRIX ORGANIZATION 0.00e+00 0.00e+00 DEGRADATION OF THE EXTRACELLULAR MATRIX 6.37e-04 7.93e-02 REGULATION OF INSULIN LIKE GROWTH FACTOR IGF ACTIVITY BY INSULIN LIKE GROWTH FACTOR BINDING PROTEINS IGFBPS 5.18e-03 4.23e-01 REGULATION OF INSULIN LIKE GROWTH FACTOR IGF ACTIVITY BY INSULIN LIKE GROWTH FACTOR BINDING PROTEINS IGFBPS 2.51e-02 1.00e+00 KERATAN SULFATE DEGRADATION 2.72e-02 1.00e+00 KERATAN SULFATE DEGRADATION 4.70e-02 1.00e+00 KERATAN SULFATE BIOSYNTHESIS 4.70e-02 1.00e+00 KERATAN SULFATE KERATIN METABOLISM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.02e-05 4.76e-02 abnormal kidney papilla morphology 2.45e-05 8.95e-02 arthritis 4.74e-05 1.38e-01 altered response to myocardial infarction 8.13e-05 1.98e-01 abnormal induced retinal neovascularization 3.99e-04 5.31e-01 decreased inflammatory response 4.94e-04 6.02e-01 impaired lung alveolus development 5.98e-04 6.73e-01 decreased length of long bones 7.13e-04 7.45e-01 increased width of hypertrophic chondrocyte zone 1.16e-03 9.82e-01 delayed wound healing 1.32e-03 1.00e+00 abnormal bronchiole morphology 1.44e-03 1.00e+00 joint inflammation 1.52e-03 1.00e+00 decreased angiogenesis 1.66e-03 1.00e+00 abnormal cartilage development 2.09e-03 1.00e+00 decreased incidence of tumors by chemical induction 2.09e-03 1.00e+00 decreased susceptibility to injury 2.32e-03 1.00e+00 abnormal long bone hypertrophic chondrocyte zone 2.33e-03 1.00e+00 abnormal trabecular bone morphology 2.71e-03 1.00e+00 decreased susceptibility to bacterial infection 2.92e-03 1.00e+00 increased susceptibility to bacterial infection 3.28e-03 1.00e+00 abnormal angiogenesis

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

²FDR corrected p-value (Benjamini-Hochberg)