MatrixDB - Extracellular Matrix interactions DataBase

Display all the molecules in a category

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

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

NEW: Construction of tissue-specific interaction networks

1987 extracellular matrix interactions including 1706 protein-protein and
111 protein-glycosaminoglycan interactions

Download MatrixDB data

in PSI-MI XML or MITAB 2.5 format

MatrixDB Tutorial

Please cite the following reference for this database:

E. Chautard, L. Ballut, N. Thierry-Mieg and S. Ricard-Blum.

MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. Bioinformatics 2009 25: 690-691. [link]

Funding:

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

MatrixDB News

MatrixDB

stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions. Interactions with lipids and cations are also reported. MatrixDB takes into account the influence of multimerization and limited cleavage on molecular recognition properties. Specific entries are created for multimers (e.g; collagens, laminins, thrombospondins) and fragments issued from extracellular matrix molecules displaying biological activities of their own (matrikins/matricryptins).

MatrixDB integrates interaction data from the Human Protein Reference Database (HPRD) with permission, from the BioGrid database, from publicly available databases of the IMEx consortium (DIP, IntAct, MINT), from in-house literature curation, and from experiments performed with protein and polysaccharide arrays probed by surface plasmon resonance (Biacore Flexchip).

MatrixDB is a member of the IMEx consortium and signed the IMEx agreement to share curation efforts. We support the Protein Standard Initiative recommendations. MatrixDB is a publicly-available database and its dataset can be freely downloaded.

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

External links:
Map of the human type I collagen fibril
Sweeney et al. (2008) J Biol Chem 283:21187-97 [link to the map] [link to the publication]
The Interaction Network of Endostatin
Faye et al. (2009) J Biol Chem 284:22041-7 [link to the map] [link to the publication]

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E-Mail for any questions or comments

Last modified: Jan 25 2010

	Browse the database Display all the molecules in a category Search by biomolecule name, dataset, PubMed Identifier, free text Interactome construction Based on localization, UniProtKB keyword(s), biomolecule name NEW: Construction of tissue-specific interaction networks Detailed statistics 1987 extracellular matrix interactions including 1706 protein-protein and 111 protein-glycosaminoglycan interactions Download MatrixDB data in PSI-MI XML or MITAB 2.5 format MatrixDB Tutorial Please cite the following reference for this database: E. Chautard, L. Ballut, N. Thierry-Mieg and S. Ricard-Blum. MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. Bioinformatics 2009 25: 690-691. [link] Funding: EU FP7 "PSIMEx" (contract number FP7-HEALTH-2007-223411) MatrixDB News		MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions. Interactions with lipids and cations are also reported. MatrixDB takes into account the influence of multimerization and limited cleavage on molecular recognition properties. Specific entries are created for multimers (e.g; collagens, laminins, thrombospondins) and fragments issued from extracellular matrix molecules displaying biological activities of their own (matrikins/matricryptins). MatrixDB integrates interaction data from the Human Protein Reference Database (HPRD) with permission, from the BioGrid database, from publicly available databases of the IMEx consortium (DIP, IntAct, MINT), from in-house literature curation, and from experiments performed with protein and polysaccharide arrays probed by surface plasmon resonance (Biacore Flexchip). MatrixDB is a member of the IMEx consortium and signed the IMEx agreement to share curation efforts. We support the Protein Standard Initiative recommendations. MatrixDB is a publicly-available database and its dataset can be freely downloaded. 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 External links: Map of the human type I collagen fibril Sweeney et al. (2008) J Biol Chem 283:21187-97 [link to the map] [link to the publication] The Interaction Network of Endostatin Faye et al. (2009) J Biol Chem 284:22041-7 [link to the map] [link to the publication]

	IBCP Home Page E-Mail for any questions or comments		Last modified: Jan 25 2010