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Fig. 1. Cytoscape version 2.0, available for free download from http://www.cytoscape.org. This screenshot shows a part of the yeast galactose metabolism network composed of protein-protein (lines) and protein-DNA (lines with arrows) interactions automatically laid out and visualized by Cytoscape. Expression data is overlaid as a black to white continuous node color gradient where black signifies low and white signifies high expression ratio between two experimental conditions. Users can navigate large networks using the "birds eye view" navigator shown at the lower left, can manage multiple networks using the network manager in the upper left panel and select visualization and analysis options using the toolbar at the top. More information about each protein and interaction in this network can be obtained using "right-click" (or context sensitive) menus when nodes or edges are selected. See the online Cytoscape manual for more information.
