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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod260

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod260 Module size 49 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 249 ALPL alkaline phosphatase, biomineralization associated 118429 ANTXR2 ANTXR cell adhesion molecule 2 85300 ATCAY ATCAY, caytaxin 135228 CD109 CD109 molecule 22918 CD93 CD93 molecule 1690 COCH cochlin 1302 COL11A2 collagen type XI alpha 2 chain 10491 CRTAP cartilage associated protein 4921 DDR2 discoidin domain receptor tyrosine kinase 2 1805 DPT dermatopontin 57119 EPPIN epididymal peptidase inhibitor 9289 GPR56 adhesion G protein-coupled receptor G1 3381 IBSP integrin binding sialoprotein 387733 IFITM5 interferon induced transmembrane protein 5 81851 KRTAP1-1 keratin associated protein 1-1 83895 KRTAP1-5 keratin associated protein 1-5 81872 KRTAP2-1 keratin associated protein 2-1 728279 KRTAP2-2 keratin associated protein 2-2 83896 KRTAP3-1 keratin associated protein 3-1 83897 KRTAP3-2 keratin associated protein 3-2 3898 LAD1 ladinin 1 3910 LAMA4 laminin subunit alpha 4 11061 LECT1 chondromodulin 55214 LEPREL1 prolyl 3-hydroxylase 2 10536 LEPREL2 prolyl 3-hydroxylase 3 4017 LOXL2 lysyl oxidase like 2 84171 LOXL4 lysyl oxidase like 4 4099 MAG myelin associated glycoprotein 4146 MATN1 matrilin 1 4147 MATN2 matrilin 2 8785 MATN4 matrilin 4 9313 MMP20 matrix metallopeptidase 20 54587 MXRA8 matrix remodeling associated 8 22795 NID2 nidogen 2 11162 NUDT6 nudix hydrolase 6 79676 OGFOD2 2-oxoglutarate and iron dependent oxygenase domain containing 2 25903 OLFML2B olfactomedin like 2B 56944 OLFML3 olfactomedin like 3 89932 PAPLN papilin, proteoglycan like sulfated glycoprotein 10631 POSTN periostin 6288 SAA2 serum amyloid A1 6291 SAA4 serum amyloid A4, constitutive 8404 SPARCL1 SPARC like 1 6695 SPOCK1 SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1 9806 SPOCK2 SPARC (osteonectin), cwcv and kazal like domains proteoglycan 2 50859 SPOCK3 SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3 80312 TET1 tet methylcytosine dioxygenase 1 338773 TMEM119 transmembrane protein 119 340706 VWA2 von Willebrand factor A domain containing 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 1.48e-01 6.38e-05 GO protein-lysine 6-oxidase activity molecular_function 1.36e-01 7.29e-10 GO growth plate cartilage chondrocyte morphogenesis biological_process 4.84e-02 6.98e-06 GO metalloendopeptidase inhibitor activity molecular_function 3.52e-02 1.04e-05 GO regulation of bone mineralization biological_process 2.81e-02 2.45e-10 GO collagen binding molecular_function 2.76e-02 6.30e-07 GO extracellular matrix binding molecular_function 6.10e-03 1.11e-07 GO collagen fibril organization biological_process 5.48e-03 1.98e-07 GO keratin filament 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 extracellular matrix 0.00e+00 0.00e+00 proteinaceous extracellular matrix 2.76e-07 1.45e-04 biomineral tissue development 7.66e-07 2.28e-04 basement membrane 1.10e-06 3.46e-04 endopeptidase inhibitor activity 1.29e-06 6.00e-04 collagen fibril organization 1.35e-06 4.18e-04 peptidase inhibitor activity 2.56e-06 6.99e-04 keratin filament 3.76e-06 1.60e-03 regulation of bone mineralization 4.19e-06 1.18e-03 collagen binding 6.22e-06 1.69e-03 calcium ion binding 9.79e-06 2.56e-03 metalloendopeptidase inhibitor activity 1.35e-05 5.06e-03 negative regulation of endopeptidase activity 1.89e-05 6.84e-03 negative regulation of peptidase activity 4.99e-05 1.13e-02 serine-type endopeptidase inhibitor activity 5.26e-05 1.68e-02 negative regulation of proteolysis 7.02e-05 2.15e-02 skin development 7.48e-05 2.27e-02 regulation of endopeptidase activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.93e-06 6.25e-04 COLLAGEN FORMATION 7.82e-06 1.52e-03 COLLAGEN FORMATION 2.04e-05 2.91e-03 EXTRACELLULAR MATRIX ORGANIZATION 4.37e-05 7.42e-03 EXTRACELLULAR MATRIX ORGANIZATION 1.38e-02 9.51e-01 BASIGIN INTERACTIONS 2.18e-02 1.00e+00 P75 NTR RECEPTOR MEDIATED SIGNALLING 2.43e-02 1.00e+00 BASIGIN INTERACTIONS 4.01e-02 1.00e+00 SIGNALLING BY NGF

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.09e-04 2.40e-01 abnormal trabecular bone morphology 2.95e-04 4.44e-01 abnormal osteoblast physiology 5.82e-04 6.64e-01 abnormal tooth morphology 7.03e-04 7.37e-01 abnormal ameloblast morphology 8.65e-04 8.31e-01 abnormal enamel morphology 8.91e-04 8.42e-01 disorganized long bone epiphyseal plate 9.10e-04 8.53e-01 decreased length of long bones 1.06e-03 9.29e-01 small cranium 1.22e-03 1.00e+00 abnormal nasal bone morphology 1.40e-03 1.00e+00 abnormal bone ossification 1.58e-03 1.00e+00 abnormal female reproductive system physiology 1.68e-03 1.00e+00 abnormal epiphyseal plate morphology 1.78e-03 1.00e+00 abnormal bone mineralization 2.02e-03 1.00e+00 decreased trabecular bone volume 2.15e-03 1.00e+00 abnormal thymus cortex morphology 2.68e-03 1.00e+00 abnormal cranium morphology 3.26e-03 1.00e+00 decreased circulating alkaline phosphatase level 3.70e-03 1.00e+00 abnormal skeleton physiology 5.40e-03 1.00e+00 abnormal long bone morphology 5.55e-03 1.00e+00 abnormal mandible morphology

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

²FDR corrected p-value (Benjamini-Hochberg)