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NetworKIN: a resource for exploring cellular phosphorylation networks.

Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T - Nucleic Acids Res. (2007)

Bottom Line: Systematically assigning all 518 human kinases to all these sites is a challenging problem.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.

View Article: PubMed Central - PubMed

Affiliation: Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada. linding@mshri.on.ca

ABSTRACT
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.

Show MeSH
Overview of the NetworKIN resource. NetworKIN starts from a set of known in vivo phosphorylation sites, which are obtained and kept synchronized with the Phospho.ELM and PhosphoSite databases to facilitate reciprocal database cross-links. We first compare these phosphorylation sites to consensus sequence motifs from the Scansite and NetPhosK resources in order to predict possible kinase families responsible for the phosphorylation. Second, we capture the kinase and substrate context using a probabilistic functional association network from the string database (12). The resulting site-specific kinase–substrate interaction network is stored in a SQL database, which is accessible via a web interface.
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Figure 1: Overview of the NetworKIN resource. NetworKIN starts from a set of known in vivo phosphorylation sites, which are obtained and kept synchronized with the Phospho.ELM and PhosphoSite databases to facilitate reciprocal database cross-links. We first compare these phosphorylation sites to consensus sequence motifs from the Scansite and NetPhosK resources in order to predict possible kinase families responsible for the phosphorylation. Second, we capture the kinase and substrate context using a probabilistic functional association network from the string database (12). The resulting site-specific kinase–substrate interaction network is stored in a SQL database, which is accessible via a web interface.

Mentions: The NetworKIN algorithm is designed to work from a set of experimentally identified in vivo phosphorylation sites (although the algorithm can also be used ab initio). The precomputed results in the database are based on the latest human phosphoproteome from the Phospho.ELM and PhosphoSite databases (2,14) (Figure 1). The release cycle of the database is approximately every 3 months due to the high throughput of mass-spectrometry-driven proteomics, and we intend to keep NetworKIN up-to-date with future releases of Phospho.ELM and PhosphoSite.Figure 1.


NetworKIN: a resource for exploring cellular phosphorylation networks.

Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T - Nucleic Acids Res. (2007)

Overview of the NetworKIN resource. NetworKIN starts from a set of known in vivo phosphorylation sites, which are obtained and kept synchronized with the Phospho.ELM and PhosphoSite databases to facilitate reciprocal database cross-links. We first compare these phosphorylation sites to consensus sequence motifs from the Scansite and NetPhosK resources in order to predict possible kinase families responsible for the phosphorylation. Second, we capture the kinase and substrate context using a probabilistic functional association network from the string database (12). The resulting site-specific kinase–substrate interaction network is stored in a SQL database, which is accessible via a web interface.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238868&req=5

Figure 1: Overview of the NetworKIN resource. NetworKIN starts from a set of known in vivo phosphorylation sites, which are obtained and kept synchronized with the Phospho.ELM and PhosphoSite databases to facilitate reciprocal database cross-links. We first compare these phosphorylation sites to consensus sequence motifs from the Scansite and NetPhosK resources in order to predict possible kinase families responsible for the phosphorylation. Second, we capture the kinase and substrate context using a probabilistic functional association network from the string database (12). The resulting site-specific kinase–substrate interaction network is stored in a SQL database, which is accessible via a web interface.
Mentions: The NetworKIN algorithm is designed to work from a set of experimentally identified in vivo phosphorylation sites (although the algorithm can also be used ab initio). The precomputed results in the database are based on the latest human phosphoproteome from the Phospho.ELM and PhosphoSite databases (2,14) (Figure 1). The release cycle of the database is approximately every 3 months due to the high throughput of mass-spectrometry-driven proteomics, and we intend to keep NetworKIN up-to-date with future releases of Phospho.ELM and PhosphoSite.Figure 1.

Bottom Line: Systematically assigning all 518 human kinases to all these sites is a challenging problem.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.

View Article: PubMed Central - PubMed

Affiliation: Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada. linding@mshri.on.ca

ABSTRACT
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.

Show MeSH