Hi everyone,
I have a list of proteins upregulated in cells under stress condition, when I compared the expression against control cells with Reactome I find some specific upregulated pathways.
My problem is that I dislike the graphical output of Reactome. Can someone suggest me a tool to obtain a better appereance for my publication? I tried to use cytoscape but I can not understand how to import properly my list of protein.
Thank you!
Hello,
I would suggest GoTermFinder http://go.princeton.edu/cgi-bin/GOTermFinder that is really easy to use. The output per se isn't nice at all but it can directly connects the output to feed REVIGO http://revigo.irb.hr/ (that in my opinion is super cool!). Besides the webtool visualization, REVIGO output an R script that, if you are familiar with it, can be easily personalize to produce very nice pictures for you publication. By the way, no matter which tool you use to get the enriched pathways in your data, you can use REVIGO anyway to make pictures.
Hope it helps.
Good luck.
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