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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.
28/06/2014: try out our new web interface! We have developed a new web interface for MatrixDB. It features a more modern look-and-feel, an all-new dynamic network navigator, and provides access to the same data.
Please try it out: http://matrixdb-new.ibcp.fr.
We would warmly welcome any feedback by email.
Display all the molecules in a category
Search by biomolecule name, dataset, PubMed Identifier, free text
- 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)
Based on localization, UniProtKB keyword(s), biomolecule name.
Construction of tissue and disease-specific interaction networks.
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.
in PSI-MI XML or MITAB 2.5 format
MatrixDB Tutorial (partly out of date)
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).
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.
Prof. Sylvie RICARD-BLUM
Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS - University Lyon 1
69367 Lyon Cedex 07 - France
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modified: Feb 09, 2014