NetworKIN: a resource for exploring cellular phosphorylation networks

By Rune Linding, Lars Juhl Jensen, A. Pasculescu, Marina Olhovsky, K. Colwill, Peer Bork, Michael B. Yaffe, Tony Pawson. Nucleic Acids Res., 2007

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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.

Subfields: Computational Theory and Mathematics, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/bb1fb194718186c4e63dadfee2dae89382dc3a2c

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Citations in the corpus

Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “The bioinformatics resources NetworKIN (http://networkin.info; Linding et al., 2007) and NetPhorest (http://netphorest.info; Miller et al., 2008) can help in the analysis cancer-related signaling changes.”
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool (2013, neutral): “Elm [35], NetworKIN [36], and MINT [37].”
Using graph theory to analyze biological networks (2011, background): “This process is modulated by many variables, such as transcription factors [24], their post-translational modifications or association with other biomole-cules [25].”
Network Medicine: A Network-based Approach to Human Disease (2011, background): “, or post-translational modifications, such as those between a kinase and its substrate”
Phospho.ELM: a database of phosphorylation sites—update 2011 (2010, background): “Since this information is relevant for gaining insights into the regulation of cellular processes, we provide direct links to NetworKIN (29), a database of predicted kinase–substrate relations.”