How to import a list of gene and visualize gene-gene interaction in Cytoscape zebrafish session

Question

[Farbod]

Dear Bisostars, Hi

I have used zebrafish (Danio rerio) when Cytoscape began to run, as my preferred network

and now I want to check for sub-network or gene-gene interaction of a list of zebrafish genes (in a text file),

BUT I don't know how and were I can import my gene names ?

Please help

~Thanks

Answer 1

[xanderpico]

Sure! You can paste you gene names into the Network Search Bar (upper left). If you have the stringApp or GeneMANIA apps installed, they'll be added to this same interface and you can directly search them the same way from within Cytoscape. Here's the manual page:

http://manual.cytoscape.org/en/stable/Creating_Networks.html#import-networks-from-public-databases

P.S. I see this is from 2.1 years ago, but Biostars has bumped it up the list... Hope it's still helpful to someone!