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Nucleic Acids Res. 2015 Jan;43(Database issue):D321-7. doi: 10.1093/nar/gku1091. Epub 2014 Nov 6.

MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities.

Author information

1
UMR 5086 CNRS - Université Lyon 1, 69367 Lyon Cedex 07, France.
2
TIMC- IMAG/BCM, UMR 5525 CNRS - Université Grenoble 1, Faculté de Médecine, 38706 La Tronche Cedex, France.
3
UMR 5086 CNRS - Université Lyon 1, 69367 Lyon Cedex 07, France s.ricard-blum@ibcp.fr.

Abstract

MatrixDB (http://matrixdb.ibcp.fr) is a freely available database focused on interactions established by extracellular proteins and polysaccharides. It is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data, either at the MIMIx or IMEx level. MatrixDB content has been updated by curation and by importing extracellular interaction data from other IMEx databases. Other major changes include the creation of a new website and the development of a novel graphical navigator, iNavigator, to build and expand interaction networks. Filters may be applied to build sub-networks based on a list of biomolecules, a specified interaction detection method and/or an expression level by tissue, developmental stage, and health state (UniGene data). Any molecule of the network may be selected and its partners added to the network at any time. Networks may be exported under Cytoscape and tabular formats and as images, and may be saved for subsequent re-use.

PMID:
25378329
PMCID:
PMC4383919
DOI:
10.1093/nar/gku1091
[Indexed for MEDLINE]
Free PMC Article

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