I didn't want to write about this one until I got these stupid manuscript edits out the door, because I needed ShinyGO and I didn't want anyone else slowing it down.
"Minor" edits done! Tool sharing time! You can read about ShinyGO here.
Don't feel like reading? You can play with ShinyGO online here!
Are there lots of tools like this out there hiding on the web? Yup! There sure are, but this honestly might be the easiest way to dig through a bunch of different resources all at once. You will need to get your protein list to universal gene identifiers or something similar (it'll translate several different types) and then you can start doing all sorts of analyses. For the figure above, I let ShinyGO select the closest related organism (ended up being Scumbag Arabidopsis) and I flipped through different databases until I got some visualizations that made my data make some sense (turned out being a nice visualization of KEGG resources with pathway representation scaled. I found that the best way to get what I wanted was to take the proteins that are up/down regulated separately and then create my network and then compare them. Worked for this model organism!
I love the fact that I can move my network nodes around and then export the image with them in that place. If you don't like that particular visualization you can export the Edges and Nodes and import them into your tool of choice.
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