Cytoscape
Cytoscape (25) is a tool for visualizing and analyzing biological networks, defined broadly to include any collection of interacting bio-molecules. A common use of the software is to display networks of protein–protein and protein–DNA interactions, but it can also be used to display gene networks. A key feature is that Cytoscape can analyze networks in combination with gene expression data, e.g. to discover sub-networks with correlated expression, and annotation data such as Gene Ontology, e.g. to associate sub-networks with biological functions.
Cytoscape can be launched directly from T1DBase, although at present this only works on two demonstration networks. Work is underway to connect Cytoscape to human protein interaction data from HPRD (26), microarray gene expression data from the Beta Cell Gene Expression Bank and other sources and annotations suggesting association with T1D susceptibility.