CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis
Fig 4
Workflow of CophosK for using co-phosphorylation to predict kinase-substrate associations (KSAs).
The method takes as input available information on KSAs and phosphorylation data representing the phosphorylation levels of thousands of phosphosites across multiple biological states. The co-phosphorylation of all pairs of phosphosites is assessed and a co-phosphorylation network is constructed in which phosphosites represent nodes and the weight of the edges is the correlation between phosphosites. CophosK then uses a Naïve Bayes classifier that integrates the interactions in this network with partial information on kinase-substrate interactions to predict new kinase substrate interaction.