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. 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.
Linding
Rune
R
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada. linding@mshri.on.ca
Jensen
Lars Juhl
LJ
Pasculescu
Adrian
A
Olhovsky
Marina
M
Colwill
Karen
K
Bork
Peer
P
Yaffe
Michael B
MB
Pawson
Tony
T
D000595:Amino Acid Sequence; D016384:Consensus Sequence; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D010750:Phosphoproteins / Q000737:chemistry* / Q000378:metabolism; D010766:Phosphorylation; D011494:Protein Kinases / Q000378:metabolism*; D040901:Proteomics; D014584:User-Computer Interface
D010750:Phosphoproteins; D011494:Protein Kinases