modENCODE Blog

In any of the gene or protein report page, modMine shows the interaction network of the gene displayed by Cytoscape Web (Lopes et al., 2010): nodes (genes) and edges (interactions) are both active links to the relevant modMine pages, and the sources of an interaction are displayed as the pointer is hovered over an edge. Different colours of edges are for different interaction types, and the network can be rendered by interaction type. Exporting the network to SIF and XGMML formats is supported.

Cytoscape Web is a web-based network visualization tool, modeled after Cytoscape, that is open source, interactive, customizable, and easily integrated into websites. Multiple file exchange formats can be used to load data into Cytoscape Web, including GraphML, XGMML and SIF. Availability and Implementation: Cytoscape Web is implemented in Flex/ActionScript with a JavaScript API and is freely available at http://cytoscapeweb.cytoscape.org/