Did I post this already? I forget. Either way, it is worth taking a look at!
Totally worth keeping in mind at all times that Perseus doesn't care what data you feed it -- it's a beautiful data package for filling with data and trying to make sense of it.
This open access review focuses on how you can use Perseus as your integration point for all sorts of omics data. This does assume (to some degree) that you can get your proteins, genes, or metabolites into some sort of a universal format so you aren't comparing things that don't make sense (which is surprisingly hard for some fields.