Figure 4.

Network analysis workflow. This workflow suggests a way to combine manual pathway data and results from network analysis. A pathway in GPML format (a) can be copied to the Cytoscape network analysis program (b) with copy and paste commands. This program is useful for viewing the pathway as a network (c) without any extra graphical annotation. The rich plug-in set of Cytoscape can be used in various ways to extend this network. If the extended network contains new information that turns out to be instructive, it may be useful to transfer part of this network (d) back to PathVisio again (e) to add manual layout and graphical annotation.