IMPORTANT UPDATE. USERS ARE URGED TO UPDATE TO 1.0.7 AS SOON AS POSSIBLE.
Due to the migration of some servers upon which the CHAT app depends, version 1.0.7 is a critical update that users are advised to immediately upgrade to. Previous versions of CHAT will shortly no longer work properly as they will be unable to access a critical file that is regularly updated.
Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape App, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes (e.g. genes or proteins that are differentially expressed) than expected by chance. In a case study, we show that such contextual hubs are considerably more biologically relevant than degree-based hubs.