Interaction Network Cytoscape

Question

[biostar.name]

Dear Cytoscape Community,

I'm working on an interaction network with Cytoscape (Version: 3.2.8) showing connections between miRNAs and targeted genes. I'm now looking for a way to filter for the gene targets, that connect at least two miRNAs with each other to reduce the number of gene targets in my network (Step 1)

Next I would like to replace these left over connecting gene targets by edges that connect only the miRNAs. My final network should then consist only of interconnected miRNAs, where the width of the edges represents the number of connecting (but invisible) gene targets (Step 2).

Is there a possible workflow/ app to get this done? I think I could handle step 1 manually by data pre-processing. Couldn't find a solution for step two though yet. Happy for your advice. Thank you for your help!

Answer 1

[scooter]

I think you can do step 2 with a little preprocessing also, but depending on the size of your network, it would probably require some scripting. In any case, I can't think of an App that does exactly what you want, unfortunately, but here is a way to think about it. You want to add an edge between any two miRNAs that are exactly two hops apart. Once that is done, you can just hide all of the gene targets (easy to do in Cytoscape). How large is your network? If it's not too large, you could do this by selecting a gene and then looking for the 2nd neighbors of that gene and add an edge, but you would need to do that for all genes. You could also use RCy3 or py4cytoscape to do that from R or python, respectively, if you are familiar with either of those scripting languages.

-- scooter