Nucleic Acids Research Advance Access originally published online on November 2, 2007
Nucleic Acids Research 2008 36(Database issue):D695-D699; doi:10.1093/nar/gkm902
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Nucleic Acids Research, 2008, Vol. 36, Database issue D695-D699
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
NetworKIN: a resource for exploring cellular phosphorylation networks
1Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada, 2Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, USA, 3The Institute of Cancer Research, London, UK, 4European Molecular Biology Laboratory, Heidelberg and 5Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
*To whom correspondence should be addressed. Tel: + 1 416 586 4800; Fax: + 1 416 586 8869; Email: linding{at}mshri.on.ca Correspondence may also be addressed to Tony Pawson. Tel: + 1 416 586 8262; Fax: + 1 416 586 8869; Email: pawson{at}mshri.on.ca
Received August 13, 2007. Revised October 3, 2007. Accepted October 4, 2007.
Protein kinases control cellular responses by phosphorylating specific substrates. Recent proteome-wide mapping of protein phosphorylation sites by mass spectrometry has discovered thousands of in vivo sites. Systematically assigning all 518 human kinases to all these sites is a challenging problem. The NetworKIN database (http://networkin.info) integrates consensus substrate motifs with context modelling for improved prediction of cellular kinase–substrate relations. Based on the latest human phosphoproteome from the Phospho.ELM and PhosphoSite databases, the resource offers insight into phosphorylation-modulated interaction networks. Here, we describe how NetworKIN can be used for both global and targeted molecular studies. Via the web interface users can query the database of precomputed kinase–substrate relations or obtain predictions on novel phosphoproteins. The database currently contains a predicted phosphorylation network with 20 224 site-specific interactions involving 3978 phosphoproteins and 73 human kinases from 20 families.
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