and another one , The Bubble Router http://www.genmapp.org/BubbleRouter/manual.htm

A cytoscape plugin for grouping nodes by 'compartment' ?

Check also Mosaic, and try to partition the network by GO Component http://apps.cytoscape.org/apps/mosaic

I agree IPA is the choice that first comes to mind. I imagine there is probably also some way to do this in cytoscape. Here is a plug-in (which, I admittedly haven't tried) that I found with quick Google search:

http://bioinformatics.oxfordjournals.org/content/23/8/1040.full

Just yesterday there was a bunch of chatter from the Biocuration meeting about Navicell. https://navicell.curie.fr/index.html I haven't tried it out yet, but I'm reading up now. They note that their foundation is the stuff you can do at CellDesigner: http://celldesigner.org/

I had forgotten about CellDesigner--that might be a way to compartmentalize your features.

Since you already work with Cytoscape, you could give the Cytoscape plugin Cerebral a try, which should be able to do this.

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