NetworKIN: a resource for exploring cellular phosphorylation networks

• Published in: Nucleic acids research Vol. 36; no. suppl-1; pp. D695 - D699
• Main Authors: Linding, Rune, Jensen, Lars Juhl, Pasculescu, Adrian, Olhovsky, Marina, Colwill, Karen, Bork, Peer, Yaffe, Michael B, Pawson, Tony
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2008; Oxford Publishing Limited (England)
• Subjects: Amino Acid Sequence; Consensus Sequence; Databases, Protein; Humans; Internet; Phosphoproteins - chemistry; Phosphoproteins - metabolism; Phosphorylation; Protein Kinases - metabolism; Proteomics; User-Computer Interface
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkm902

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.