MatrixDB - Extracellular Matrix interactions DataBase

Display all the molecules in a category

Search by biomolecule name, dataset, PubMed Identifier, free text

Interaction datasets:
- The extracellular LRR and IgSF neuroreceptor interaction network (Bushell et al. 2008 Genome Res. 18:622-30; Söllner et al. 2009 Genome Biol. 10:R99)
- The elastic fiber interactome (Cain et al. 2009 Mol Cell Proteomics. 8:2715-32)
- The interaction network of endostatin (Faye et al. 2009 J Biol Chem. 284:22041-7)

New protein links: direct links to OMIM, to UniGene and to the Human Protein Atlas databases

Interactome construction

Based on localization, UniProtKB keyword(s), biomolecule name

NEW: Construction of tissue and disease-specific interaction networks

Detailed statistics

2174 extracellular matrix interactions including 1836 protein-protein and
119 protein-glycosaminoglycan interactions

Download MatrixDB data

in PSI-MI XML or MITAB 2.5 format

MatrixDB Tutorial

MatrixDB publications

MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. Chautard E, Ballut L, Thierry-Mieg N, Ricard-Blum S. Bioinformatics 2009 25: 690-691. [abstract]
MatrixDB, the extracellular matrix interaction database. Chautard E, Fatoux-Ardore M, Ballut L, Thierry-Mieg N, Ricard-Blum S. Nucleic Acids Res. 2011; 39:D235-40. [abstract]

Funding:

EU FP7 "PSIMEx"
(contract number FP7-HEALTH-2007-223411)

MatrixDB News

MatrixDB is a freely available database focused on interactions established by extracellular proteins and polysaccharides. Only few databases report protein-polysaccharide interactions and to the best of our knowledge, there is no other interaction database focused on the extracellular matrix. Furthermore, MatrixDB takes into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). This is a concern when molecules are heterotrimeric and/or when the multimerization process modifies the molecular recognition properties. MatrixDB reports interaction with individual polypeptide chains or with multimers (permanent complexes) when appropriate.
Data stored in MatrixDB include experimental data from our laboratory, data extracted from the literature by manual curation, data exchanged with IMEx databases (IntAct, DIP, MINT, and BioGRID databases), and data from the Human Protein Reference Database. Data imported from other databases are restricted to extracellular proteins and their partners.

MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data.
MatrixDB is in charge of the curation of papers published in Matrix Biology since January 2009.

External links:
Laminin database: a tool to retrieve high-throughput and curated data for studies on laminins
Golbert et al. (2011) Nucleic Acids Res. 39:D320-3 [abstract]
The Interaction Network of Endostatin
Faye et al. (2009) J Biol Chem 284:22041-7 [link to the map] [abstract]
COLdb, a database linking genetic data to molecular function in fibrillar collagens
Bodian and Klein (2009) Hum Mutat. 30:946-591 [link to the database] [abstract]
Map of the human type I collagen fibril
Sweeney et al. (2008) J Biol Chem 283:21187-97 [link to the map] [abstract]
Osteogenesis Imperfecta Mutation Consortium Review
Marini et al. (2007) Hum. Mutat. 28:209-221 [link to the database] [abstract]
Osteogenesis imperfecta & Ehlers-Danlos syndrome variant databases
Dalgleish (1997) Nucleic Acids Res. 25:181-7 [link to the database] [abstract]
Dalgleish (1998) Nucleic Acids Res. 26:253-5 [link to the database] [abstract]

Contact

Prof. Sylvie RICARD-BLUM
Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS - University Lyon 1
69367 Lyon Cedex 07 - France
e-mail: matrixdb@ibcp.fr

IBCP Home Page
E-Mail for any questions or comments

Last modified: Aug 26, 2010

	Browse the database Display all the molecules in a category Search by biomolecule name, dataset, PubMed Identifier, free text Interaction datasets: - The extracellular LRR and IgSF neuroreceptor interaction network (Bushell et al. 2008 Genome Res. 18:622-30; Söllner et al. 2009 Genome Biol. 10:R99) - The elastic fiber interactome (Cain et al. 2009 Mol Cell Proteomics. 8:2715-32) - The interaction network of endostatin (Faye et al. 2009 J Biol Chem. 284:22041-7) New protein links: direct links to OMIM, to UniGene and to the Human Protein Atlas databases Interactome construction Based on localization, UniProtKB keyword(s), biomolecule name NEW: Construction of tissue and disease-specific interaction networks Detailed statistics 2174 extracellular matrix interactions including 1836 protein-protein and 119 protein-glycosaminoglycan interactions Download MatrixDB data in PSI-MI XML or MITAB 2.5 format MatrixDB Tutorial MatrixDB publications MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. Chautard E, Ballut L, Thierry-Mieg N, Ricard-Blum S. Bioinformatics 2009 25: 690-691. [abstract] MatrixDB, the extracellular matrix interaction database. Chautard E, Fatoux-Ardore M, Ballut L, Thierry-Mieg N, Ricard-Blum S. Nucleic Acids Res. 2011; 39:D235-40. [abstract] Funding: EU FP7 "PSIMEx" (contract number FP7-HEALTH-2007-223411) MatrixDB News		MatrixDB is a freely available database focused on interactions established by extracellular proteins and polysaccharides. Only few databases report protein-polysaccharide interactions and to the best of our knowledge, there is no other interaction database focused on the extracellular matrix. Furthermore, MatrixDB takes into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). This is a concern when molecules are heterotrimeric and/or when the multimerization process modifies the molecular recognition properties. MatrixDB reports interaction with individual polypeptide chains or with multimers (permanent complexes) when appropriate. Data stored in MatrixDB include experimental data from our laboratory, data extracted from the literature by manual curation, data exchanged with IMEx databases (IntAct, DIP, MINT, and BioGRID databases), and data from the Human Protein Reference Database. Data imported from other databases are restricted to extracellular proteins and their partners. MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. MatrixDB is in charge of the curation of papers published in Matrix Biology since January 2009. External links: Laminin database: a tool to retrieve high-throughput and curated data for studies on laminins Golbert et al. (2011) Nucleic Acids Res. 39:D320-3 [abstract] The Interaction Network of Endostatin Faye et al. (2009) J Biol Chem 284:22041-7 [link to the map] [abstract] COLdb, a database linking genetic data to molecular function in fibrillar collagens Bodian and Klein (2009) Hum Mutat. 30:946-591 [link to the database] [abstract] Map of the human type I collagen fibril Sweeney et al. (2008) J Biol Chem 283:21187-97 [link to the map] [abstract] Osteogenesis Imperfecta Mutation Consortium Review Marini et al. (2007) Hum. Mutat. 28:209-221 [link to the database] [abstract] Osteogenesis imperfecta & Ehlers-Danlos syndrome variant databases Dalgleish (1997) Nucleic Acids Res. 25:181-7 [link to the database] [abstract] Dalgleish (1998) Nucleic Acids Res. 26:253-5 [link to the database] [abstract] Contact Prof. Sylvie RICARD-BLUM Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS - University Lyon 1 69367 Lyon Cedex 07 - France e-mail: matrixdb@ibcp.fr

	IBCP Home Page E-Mail for any questions or comments		Last modified: Aug 26, 2010