HTML tutorial



Python Script


Contextual Hub Analysis Tool (CHAT)

The Contextual Hubs Analysis Tool (CHAT) enables users to easily construct and visualize a network of interactions from a list of genes of interest; integrate contextual information such as gene expression data; and to identify nodes that are more highly connected to contextual nodes (e.g. differentially expressed nodes) than expected by chance. CHAT is available as a fully-featured command line tool and an online GUI. To use CHAT users have two options:

  1. They can provide a pre-constructed network with contextual node attribute data in XGMML format. XGMML files can be exported from the widely used Cytoscape software or downloaded after completing a network analysis in To use this option click "Upload Network".
  2. Alternatively, the user can provide CHAT with a list of human or mouse Ensembl Gene IDs and a network will be constructed using the complete set of human or mouse interaction data available through InnateDB (i.e. not just innate immunity relevant interactions). To use this option click "Build Network".
Before starting we recommend you take a look at the short tutorial – it will save you time in the long-run!

To begin the user may click "Build Network" below to query a list of genes with contextual confidence information (e.g. P-values, Fold Change) directly or click "Upload Network" to query a prepared network in Cytoscape format (.xgmml) that has contextual confidence information attached as node attributes. For optimal performance we recommend Chrome or IE web browsers (see

?       OR ?
Primes Project Logo SFI Logo FP7 Logo

The research leading to these results received funding from the European Union Seventh Framework Programme (FP7/2007-2013) PRIMES project grant FP7-HEALTH-2011-278568 & Science Foundation Ireland grant 09/IN.1/B2642.

Developed by the Lynn EMBL Australia Group.