--HOME-- Browse the database Interactome Construction Download Tutorial - Help
 MatrixDB banner
 
WORK IN PROGRESS
14/04/2014: the complete MatrixDB content has been updated. We also improved the database schema, streamlined several of our processes, and fixed many inconsistencies or errors in the data itself. Because this is a major update, some functionalities of this web-site may have been impacted despite our testing. If something looks broken please email us about it so we can fix it! Thank you for your help and patience.

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.
Construction of tissue and disease-specific interaction networks.

Statistics
Via in-house literature curation, MatrixDB provides 821 extracellular matrix interactions from 1065 individual experiments reported in 215 publications.
Additionnally we import ECM-related interactions from our partner IMEx databases, so that in total MatrixDB holds  8244 interactions supported by 14755 experiments.

Download MatrixDB data
in PSI-MI XML or MITAB 2.5 format

MatrixDB Tutorial (partly out of date)


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:
IXXI  Rhone-Alpes  EU  EU FP7 "PSIMEx"
(contract number FP7-HEALTH-2007-223411)


RSS_logo MatrixDB News

 

MatrixDB is a freely available database focused on interactions established by extracellular proteins and polysaccharides.
MatrixDB takes into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers).
imex
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 includes interaction data extracted from the literature by manual curation in our lab, and offers access to relevant data involving extracellular proteins provided by our IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database.

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 [link to the database] [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: Feb 09, 2014
Valid XHTML 1.0 Strict CSS Valide !