To implement the web-based system we use Java Server Pages (JSP) and MySQL database running on a Tomcat server. All reported results can be exported to Excel via CSV files. Additionally, users can mouse over on the number of targets for each kinase, kinase family or class to see the list of substrates and view a connectivity diagram that visualizes known protein–protein interactions within the substrates using a database of protein–protein interactions we previously published (Berger et al., 2007). The map is dynamic where users can move nodes around and click on nodes for more detail (Fig. 1). The visualization of these connectivity diagrams was achieved using Adobe Flash CS4 with ActionScript. Such subgraphs can be used to link kinase specific substrates to pathways and complexes.
Fig. 1. Screenshot of the KEA user interface. Users can paste lists of Entrez gene symbols, representing human proteins; select the level of analysis: kinase-class, kinase-family or kinase and then the program outputs a list of ranked kinase-classes, kinase-families or kinases based on specificity of phosphorylating substrates from the input list. Substrates can be then connected based on their known protein–protein interaction using an original network viewer developed using Adobe Flash CS4.