MatrixDB, the extracellular matrix interaction database

Abstract

MatrixDB (http://matrixdb.ibcp.fr) 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 database of extracellular interactions. MatrixDB takes into account the multimeric nature of several extracellular protein families for the curation of interactions, and reports interactions with individual polypeptide chains or with multimers, considered as permanent complexes, when appropriate. MatrixDB is a member of the International Molecular Exchange consortium (IMEx) and has adopted the PSI-MI standards for the curation and the exchange of interaction data. MatrixDB stores experimental data from our laboratory, data from literature curation, data imported from IMEx databases, and data from the Human Protein Reference Database. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa.

Figure 1.

Organization of MatrixDB showing the sources of biomolecule and interaction data, the ‘Biomolecule Report’, ‘Interaction Report’ and ‘Experiment Report’ pages, the links to other web sites, the construction of interaction networks, data formats available for downloading and data exchange with the members of the IMEx consortium.

Figure 2.

Protein–protein interaction networks of skin (A) and brain (B), built using MatrixDB and visualized with Cytoscape (threshold used for UniGene annotations: ≥100 transcripts per million). Edges: interactions. Pink nodes: proteins specific of skin (A) or brain (B); blue nodes: proteins present in five tissues (liver, lung, bone, skin and brain); grey nodes: other proteins present in two to four tissues out of five.