Cytoscape help

We have developed an easy-to-use query and visualization system to represent our interactome. The discussed protein clusters as well as the complete predicted interactome can be observed through a web-start version of Cytoscape. A node and edge attribute system is employed to represent the different types of information. The color of the edge represents the degree of co-expression calculated as the Pearson correlation coefficient, the line width of the edge represents the GO biological process similarity score and the line style of the edge represents the GO cellular component similarity score. The color of the nodes corresponds to the CAST cluster the protein belongs to. TAIR functional descriptions are shown as node labels. Subsets of the interactome that are of interest to the researcher can be visualized easily by querying the interactome for (a) protein(s) or for a functional description.