Is there an easy way to make a secondary ppi network in cytoscape? Or is it only possible by downloading all ppi networks of the primary protein and then assemble them manually? And if I would do it manually whats a good way to select proteins that are significant for said network?
EDIT: expanding a network in a way that it includes all interaction partners of the first interaction partners of 1 protein
And by a secondary PPI network you mean adding information from an existing interaction network (database) to your primary one? If that is what you mean you might want to check out our new CyTargetLinker app (plugin) for Cytoscape. Which is available here: http://apps.cytoscape.org/apps/cytargetlinker. Usually TF, miRNA or drug target relations are used for the secondary network (hence the name), but it comes with scripts to build your own secondary network source. The project home page is here.
Actually what I meant was expanding a network in a way that it includes all interaction partners of the first interaction partners of 1 protein. But the plugin you have suggested seems useful to select the useful interactions.
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