MatrixDB explained

MatrixDB
Description:extracellular matrix interactions database.
Scope:Interactions DataBase, Biochemestry, Biacore, SPR
Organism:All (Human only possible)
Laboratory:IBCP - UMR5086 CNRS / Univ Lyon1 - FRANCE
Author:Emilie Chautard, Guillaume Launay, Nicolas Thierry-Mieg, Romain Salza, Franck Peysselon, Marie Fatoux-Ardore, Sofiane Badaoui, Sylvain Vallet, Lionel Ballut, Dorian Multedo, Sylvie Ricard-Blum.
Pmid:20852260
Standard:PSI-MI
Url:http://matrixdb.univ-lyon1.fr

MatrixDB is a biological database focused on molecular interactions between extracellular proteins and polysaccharides.[1] MatrixDB takes into account the multimeric nature of the extracellular proteins (for example, collagens, laminins and thrombospondins are multimers). The database was initially released in 2009[2] and is maintained by the research group of Sylvie Ricard-Blum at UMR5246, Claude Bernard University Lyon 1.

MatrixDB is linked with UniGene and the Human Protein Atlas. It also allows users to build customised tissue- and disease-specific interaction networks, which can be further analysed and visualised using Cytoscape or Medusa.

MatrixDB is an active member of the International Molecular Exchange Consortium (IMEx),[3] a group of the major public providers of interaction data. Other participating databases include the Biomolecular Interaction Network Database (BIND),[4] IntAct,[5] the Molecular Interaction Database (MINT),[6] MIPS,[7] MPact, and BioGRID. The databases of IMEx work together to prevent duplications of effort, collecting data from non-overlapping sources and sharing the curated interaction data. The IMEx consortium also worked to develop the HUPO-PSI-MI XML standard format for annotating and exchanging interaction data.[8] MatrixDB includes interaction data extracted from the literature by manual curation and offers access to relevant data involving extracellular proteins provided by IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database.

External links

Notes and References

  1. Chautard. E.. Fatoux-Ardore. M.. Ballut. L.. Thierry-Mieg. N.. Ricard-Blum. S.. MatrixDB, the extracellular matrix interaction database. Nucleic Acids Research. 17 September 2010. 39. Database. D235–D240. 10.1093/nar/gkq830. 20852260. 3013758.
  2. Chautard. E.. Ballut. L.. Thierry-Mieg. N.. Ricard-Blum. S.. MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. Bioinformatics. 15 January 2009. 25. 5. 690–691. 10.1093/bioinformatics/btp025. 19147664. 2647840.
  3. Orchard . S. . Kerrien . S. . Abbani . S. . Aranda . B. . Bhate . J. . Bidwell . S. . Bridge . A. . Briganti . L. . Brinkman . F. . Cesareni . 10.1038/nmeth.1931 . G. . Chatr-Aryamontri . A. . Chautard . E. . Chen . C. . Dumousseau . M. . Goll . J. . Hancock . R. . Hannick . L. I. . Jurisica . I. . Khadake . J. . Lynn . D. J. . Mahadevan . U. . Perfetto . L. . Raghunath . A. . Ricard-Blum . S. . Roechert . B. . Salwinski . L. . Stümpflen . V. . Tyers . M. . Uetz . P. . Xenarios . I. . Protein interaction data curation: The International Molecular Exchange (IMEx) consortium . Nature Methods . 9 . 4 . 345–350 . 2012 . 22453911 . 3703241 .
  4. Alfarano. C.. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Research. 17 December 2004. 33. Database issue. D418–D424. 10.1093/nar/gki051. 15608229. 540005.
  5. Kerrien. S.. Aranda. B.. Breuza. L.. Bridge. A.. Broackes-Carter. F.. Chen. C.. Duesbury. M.. Dumousseau. M.. Feuermann. M.. Hinz. U.. Jandrasits. C.. Jimenez. R. C.. Khadake. J.. Mahadevan. U.. Masson. P.. Pedruzzi. I.. Pfeiffenberger. E.. Porras. P.. Raghunath. A.. Roechert. B.. Orchard. S.. Hermjakob. H.. The IntAct molecular interaction database in 2012. Nucleic Acids Research. 24 November 2011. 40. D1. D841–D846. 10.1093/nar/gkr1088. 22121220. 3245075.
  6. Zanzoni. A. Montecchi-Palazzi. L. Quondam. M. Ausiello. G. Helmer-Citterich. M. Cesareni. G. MINT: a Molecular INTeraction database.. FEBS Letters. Feb 20, 2002. 513. 1. 135–40. 11911893. 10.1016/s0014-5793(01)03293-8. 1751541.
  7. Guldener. U.. MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Research. 1 January 2006. 34. 90001. D436–D441. 10.1093/nar/gkj003. 16381906. 1347366.
  8. Hermjakob. Henning. Montecchi-Palazzi. Luisa. Bader. Gary. Wojcik. Jérôme. Salwinski. Lukasz. Ceol. Arnaud. Moore. Susan. Orchard. Sandra. Sarkans. Ugis. von Mering. Christian. Roechert. Bernd. Poux. Sylvain. Jung. Eva. Mersch. Henning. Kersey. Paul. Lappe. Michael. Li. Yixue. Zeng. Rong. Rana. Debashis. Nikolski. Macha. Husi. Holger. Brun. Christine. Shanker. K. Grant. Seth G N. Sander. Chris. Bork. Peer. Zhu. Weimin. Pandey. Akhilesh. Brazma. Alvis. Jacq. Bernard. Vidal. Marc. Sherman. David. Legrain. Pierre. Cesareni. Gianni. Xenarios. Ioannis. Eisenberg. David. Steipe. Boris. Hogue. Chris. Apweiler. Rolf. The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data. Nature Biotechnology. 2004. 22. 2. 177–183. 10.1038/nbt926. 14755292. 17557764.

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