Link pathways to Gene Onthologies from RNA-seq differential expressed genes

Question

[lucatucciarone]

Hello everybody!

I was thinking whether existed a way to link a pathway to a GO-term (Biological process).

For example, let's say I have MTOR signalling activated, I know from the literature that is linked with cell growth. Is there a way to compute all those relationships?

Thanks!

[jared.andrews07]

Where are you getting your pathways from?

[lucatucciarone]

Hello Jared! Thanks for helping me again : )

I got my pathways from IPA. Unfortunately though, IPA doesn't give me a clear idea of what biological process a specific pathway is activating or inhibiting.

What I'd like to do is: 1) Performing Pathway analysis using the differentially expressed genes (Directional pathway analysis, I need a Z-score) 2) Clustering the most significantly modulated pathways hierarchically, based on what biological process they are modulating

[jared.andrews07]

Does it give you any sort of identifier for the pathway besides the name? There may be a way to look them up if so.

[lucatucciarone]

Unfortunately not, it's from the IPA knowledgeabase.

I wanna say I'm not married to IPA, I can definitely switch to another tool if it would allow me to do what I'd like to : )

[jared.andrews07]

Oof, I'd probably switch to something that gives an identifier then. KEGG or Reactome or Panther or something.

[lucatucciarone]

Marvelous, and after I have an identifier how can I link it to a certain Biological Process?