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NetworKIN: a resource for exploring cellular phosphorylation networks.

Rune Linding1, Lars Juhl Jensen, Adrian Pasculescu

  • 1Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada. linding@mshri.on.ca

Nucleic Acids Research
|November 6, 2007
PubMed
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NetworKIN predicts kinase-substrate interactions using motifs and context. This resource aids in understanding cellular signaling networks by mapping protein phosphorylation sites to specific kinases.

Area of Science:

  • Biochemistry
  • Systems Biology
  • Bioinformatics

Background:

  • Protein kinases are crucial regulators of cellular processes through substrate phosphorylation.
  • Recent advances in mass spectrometry have identified thousands of in vivo phosphorylation sites.
  • Assigning specific kinases to these numerous sites presents a significant challenge in cell biology.

Purpose of the Study:

  • To present NetworKIN, a database and web tool for predicting kinase-substrate relationships.
  • To integrate consensus substrate motifs with contextual information for enhanced prediction accuracy.
  • To provide insights into phosphorylation-modulated interaction networks based on current phosphoproteome data.

Main Methods:

  • Utilizing consensus substrate motifs derived from databases like Phospho.ELM and PhosphoSite.

Related Experiment Videos

  • Employing context modeling to refine predictions of kinase-substrate interactions.
  • Developing a web interface for querying precomputed relations and predicting novel phosphoproteins.

    • Main Results:

    • The NetworKIN database contains a predicted phosphorylation network of 20,224 site-specific interactions.
    • These interactions involve 3978 phosphoproteins and 73 human kinases from 20 families.
    • The resource facilitates both global and targeted molecular studies of phosphorylation.

    Conclusions:

    • NetworKIN offers a valuable resource for exploring kinase-substrate interactions and cellular signaling.
    • The database aids researchers in understanding the functional roles of protein phosphorylation.
    • It enables predictions for novel phosphoproteins, advancing phosphoproteomics research.