Cytoscape, is there a way to load a disease pathway and then eliminate a gene (ko) to understand it's affect on the pathway?
Hello,
Yes it is possible.
Let us consider the pathway be XY.
You first extract all the proteins in the pathway XY by using KEGG, reactome database etc.
You can use STRING to construct a network of these proteins. Extract the network and import them to cytoscape.
Now, calculate the topological property of the network. .
Omit a node.
And calculate the topological property again to compare the both network.
When we omit a node, the edges corresponding to that node will also get omitted which will alter the topological property of the network.
A comparison of both will help to understand the effect topologically.
Hi Dipanka,
Thank you very much for your detailed explanation. I ended up importing a network for CRC cancer from strong DB. This is (I believe an undirected network). When I wanted to run Analyze Network, I got a wizard that asks me "Analyze as Direct Graph" when I check this box and say ok I get an error saying"NetworkInterpretatiin is null". Any idea what this means? Is there a webpage where I can find explanation to all errors? Much obliged, Sharon
Sharon Shechter Hello. I have never experienced that error hence can't say much about that. Could you please provide some more information like your Cytoscape version, the format of the data input file (.xlsx .csv, etc).??
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