MatrixDB
 | |
| Content | |
|---|---|
| Description | extracellular matrix interactions database. |
| Data types captured | Interactions DataBase, Biochemestry, Biacore, SPR |
| Organisms | All (Human only possible) |
| Contact | |
| Laboratory | IBCP - UMR5086 CNRS / Univ Lyon1 - FRANCE |
| Authors | 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. |
| Primary citation | PMID 20852260 |
| Access | |
| Standards | PSI-MI |
| Website | 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.[1]
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.[3] 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.[3][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.
References
[edit]- ^ a b Chautard, E.; Fatoux-Ardore, M.; Ballut, L.; Thierry-Mieg, N.; Ricard-Blum, S. (17 September 2010). "MatrixDB, the extracellular matrix interaction database". Nucleic Acids Research. 39 (Database): D235–D240. doi:10.1093/nar/gkq830. PMC 3013758. PMID 20852260.
- ^ Chautard, E.; Ballut, L.; Thierry-Mieg, N.; Ricard-Blum, S. (15 January 2009). "MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions". Bioinformatics. 25 (5): 690–691. doi:10.1093/bioinformatics/btp025. PMC 2647840. PMID 19147664.
- ^ a b c Orchard, S.; Kerrien, S.; Abbani, S.; Aranda, B.; Bhate, J.; Bidwell, S.; Bridge, A.; Briganti, L.; Brinkman, F.; Cesareni, 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. (2012). "Protein interaction data curation: The International Molecular Exchange (IMEx) consortium". Nature Methods. 9 (4): 345–350. doi:10.1038/nmeth.1931. PMC 3703241. PMID 22453911.
- ^ Alfarano, C. (17 December 2004). "The Biomolecular Interaction Network Database and related tools 2005 update". Nucleic Acids Research. 33 (Database issue): D418–D424. doi:10.1093/nar/gki051. PMC 540005. PMID 15608229.
- ^ 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. (24 November 2011). "The IntAct molecular interaction database in 2012". Nucleic Acids Research. 40 (D1): D841–D846. doi:10.1093/nar/gkr1088. PMC 3245075. PMID 22121220.
- ^ Zanzoni, A; Montecchi-Palazzi, L; Quondam, M; Ausiello, G; Helmer-Citterich, M; Cesareni, G (Feb 20, 2002). "MINT: a Molecular INTeraction database". FEBS Letters. 513 (1): 135–40. doi:10.1016/s0014-5793(01)03293-8. PMC 1751541. PMID 11911893.
- ^ Guldener, U. (1 January 2006). "MPact: the MIPS protein interaction resource on yeast". Nucleic Acids Research. 34 (90001): D436–D441. doi:10.1093/nar/gkj003. PMC 1347366. PMID 16381906.
- ^ 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 (2004). "The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data". Nature Biotechnology. 22 (2): 177–183. doi:10.1038/nbt926. PMID 14755292. S2CID 17557764.