Visualize pathways from MSigDB

Question

[Chris]

Hi Biostars,

I have some pathways of interested from MSigDB and would like to visualize them if they share common genes. Cnetplot can make a nice network plot but only for GO term from gene set enrichment analysis. Would you please have a suggestion? Cytoscape can do the job the resolution of figure is low. Could we make plot with color of node present level of expression like in cnetplot? Thank you so much!

Answer 1

[jared.andrews07]

I expect this is pretty trivial in cytoscape.

[Chris]

Yes, I looked at cytoscape and not sure which app in this store to use. Would you recommend a suitable one?

[jared.andrews07]

I haven't used cytoscape in ages, but at a glance, there seem to be a ton of them that'd work. Once you get your data into cytoscape as nodes and edges appropriately, it should be pretty easy to try a handful of them to see which give you a visual that you like.