I am working with a non-model organism (Durusdinium trenchii) whose proteome I have annotated through the STRING "Annotate your Proteome" program. I have a list of 2,500 proteins that I would like to upload to STRING using this proteome, but I get the error "STRING website does not support networks larger than 2000 nodes. In order to visualize large STRING networks please use our Cytoscape stringApp", which I also have. My question is this: am I somehow able to upload my STRING-annotated proteome for use in this app?
(I know that 2,500 genes is a lot, and I just need the interaction network in order to run a hub gene analysis (also on Cytoscape) to find the top 5 most connected genes. Since D. trenchii is not an organism on the Cytoscape stringApp I have been unable to get anywhere with this problem.)
Unfortunately, the stringApp doesn't support the "Annotate your Proteome" networks at this point. According to the documentation, it looks like you can download your entire proteome by going to string download page (rather than try to query for it). Give that a try...