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MatrixDB, the extracellular matrix interaction database.

Nucleic acids research | Jan 23, 2011

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.

Pubmed ID: 20852260 RIS Download

Mesh terms: Animals | Databases, Protein | Extracellular Matrix Proteins | Humans | Mutation | Polysaccharides | Protein Interaction Mapping

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UniGene

Database access to computationally identified transcripts from the same locus; analyzed expression by tissue, age, and health status; and reports related proteins (protEST) and clone resources. In addition to sequences of well-characterized genes, hundreds of thousands novel expressed sequence tag (EST) sequences have been included. Consequently, the collection may be of use to the community as a resource for gene discovery. UniGene has also been used by experimentalists to select reagents for gene mapping projects and large-scale expression analysis. A representation of the UniGene datasets is available by ftp.

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