This is a post to better understand what is your favorite tool to perform gene ontology for biological processes from differentially expressed genes (RNA-seq Data).

There are a lot of tools over the internet, for now I'm been using IPA (Luckily my institute has a subscription) but I find it sometimes not completely coherent.

To make you better understand what I'm searching for, in the dream world I would need (From differentially expressed genes) one or more tools that would:

1) Give me a z-score list of the most modulated biological functions 2) Understand what are the pathways that modulate those functions 3) Understand the "Up-stream reagulators" of those pathways that modulates the functions above.

I know that IPA, in theory, can exactly do that, but once again, I don't see a lot of coherence in my experience with it!