NetworKIN: a resource for exploring cellular phosphorylation networks
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....
| Main Authors: | , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Oxford University Press (OUP)
2012
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| Online Access: | http://hdl.handle.net/1721.1/70998 https://orcid.org/0000-0002-9547-3251 |
| _version_ | 1826199275517771776 |
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| author | Jensen, Lars Juhl Pasculescu, Adrian Olhovsky, Marina Colwill, Karen Bork, Peer Pawson, Tony Linding, Rune Yaffe, Michael B |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Jensen, Lars Juhl Pasculescu, Adrian Olhovsky, Marina Colwill, Karen Bork, Peer Pawson, Tony Linding, Rune Yaffe, Michael B |
| author_sort | Jensen, Lars Juhl |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T11:17:29Z |
| format | Article |
| id | mit-1721.1/70998 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T11:17:29Z |
| publishDate | 2012 |
| publisher | Oxford University Press (OUP) |
| record_format | dspace |
| spelling | mit-1721.1/709982022-09-27T18:27:58Z NetworKIN: a resource for exploring cellular phosphorylation networks Jensen, Lars Juhl Pasculescu, Adrian Olhovsky, Marina Colwill, Karen Bork, Peer Pawson, Tony Linding, Rune Yaffe, Michael B Massachusetts Institute of Technology. Department of Biology Yaffe, Michael B. Linding, Rune Yaffe, Michael B. 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. Genome Canada (through Ontario Genomics Institute) National Institutes of Health (U.S.) (U54-CA112967) National Institutes of Health (U.S.) (GM60594) European Community’s Human Potential Programme (BioSapiens Network of Excellence (contract number LSHG-CT-2003-503265)) European Community’s Human Potential Programme (ADIT Integrated Project (contract number LSHB-CT-2005511065)) 2012-06-01T20:25:15Z 2012-06-01T20:25:15Z 2007-11 2007-10 Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 http://hdl.handle.net/1721.1/70998 Linding, R. et al. “NetworKIN: a Resource for Exploring Cellular Phosphorylation Networks.” Nucleic Acids Research 36.Database (2007): D695–D699. Web. 1 June 2012. https://orcid.org/0000-0002-9547-3251 en_US http://dx.doi.org/10.1093/nar/gkm902 Nucleic Acids Research Creative Commons Attribution Non-Commercial http://creativecommons.org/licenses/by-nc/2.5 application/pdf Oxford University Press (OUP) Oxford |
| spellingShingle | Jensen, Lars Juhl Pasculescu, Adrian Olhovsky, Marina Colwill, Karen Bork, Peer Pawson, Tony Linding, Rune Yaffe, Michael B NetworKIN: a resource for exploring cellular phosphorylation networks |
| title | NetworKIN: a resource for exploring cellular phosphorylation networks |
| title_full | NetworKIN: a resource for exploring cellular phosphorylation networks |
| title_fullStr | NetworKIN: a resource for exploring cellular phosphorylation networks |
| title_full_unstemmed | NetworKIN: a resource for exploring cellular phosphorylation networks |
| title_short | NetworKIN: a resource for exploring cellular phosphorylation networks |
| title_sort | networkin a resource for exploring cellular phosphorylation networks |
| url | http://hdl.handle.net/1721.1/70998 https://orcid.org/0000-0002-9547-3251 |
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