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MatrixDB, the extracellular matrix interaction database
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 interactio...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013758/ https://www.ncbi.nlm.nih.gov/pubmed/20852260 http://dx.doi.org/10.1093/nar/gkq830 |
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author | Chautard, Emilie Fatoux-Ardore, Marie Ballut, Lionel Thierry-Mieg, Nicolas Ricard-Blum, Sylvie |
author_facet | Chautard, Emilie Fatoux-Ardore, Marie Ballut, Lionel Thierry-Mieg, Nicolas Ricard-Blum, Sylvie |
author_sort | Chautard, Emilie |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-3013758 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-30137582011-01-03 MatrixDB, the extracellular matrix interaction database Chautard, Emilie Fatoux-Ardore, Marie Ballut, Lionel Thierry-Mieg, Nicolas Ricard-Blum, Sylvie Nucleic Acids Res Articles 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. Oxford University Press 2011-01 2010-09-17 /pmc/articles/PMC3013758/ /pubmed/20852260 http://dx.doi.org/10.1093/nar/gkq830 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Chautard, Emilie Fatoux-Ardore, Marie Ballut, Lionel Thierry-Mieg, Nicolas Ricard-Blum, Sylvie MatrixDB, the extracellular matrix interaction database |
title | MatrixDB, the extracellular matrix interaction database |
title_full | MatrixDB, the extracellular matrix interaction database |
title_fullStr | MatrixDB, the extracellular matrix interaction database |
title_full_unstemmed | MatrixDB, the extracellular matrix interaction database |
title_short | MatrixDB, the extracellular matrix interaction database |
title_sort | matrixdb, the extracellular matrix interaction database |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013758/ https://www.ncbi.nlm.nih.gov/pubmed/20852260 http://dx.doi.org/10.1093/nar/gkq830 |
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