How to create circle network of multiple pathways

[Sam]

I obtained a list of genes through a pre-ranked GSEA for 3 drugs and would like to determine which pathways are overrepresented, with a degree-sorted circular layout plot consisting of nodes that represent major sub-pathways and edges that represent genetic interactions in humans.  I have Cytoscape 3.3.0 and have downloaded the reactome 5 plugin.  1) Can I perform a second enrichment analysis with reactome to determine the significant pathways involved (after having done a pre-ranked GSEA), or should I import the first enriched gene list into cytoscape to simply overlay unto another network?  2) I can view diagrams for specific sub-pathways, convert to FI network, but I am unable to create a compiled figure for all the pathways.  How to create a circular layout like Figure 5, as previously published, http://www.nature.com/nrc/journal/v15/n3/abs/nrc3891.html?

[alex.pico]

Hi Saima,

Some of these questions might be better answered by the authors of the Reactome FI App (cc'd). If you question is about the specific protocol of steps to reproduce the Figure you link to, you should also consider contacting the paper authors directly. But, in terms of  Cytoscape basics, yes, it has degree-sorted circle layout that should work once you have the network constructed.
 
 - Alex