Question: Link pathways to Gene Onthologies from RNA-seq differential expressed genes
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gravatar for lucatucciarone
4 weeks ago by
lucatucciarone50 wrote:

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!

rna-seq • 118 views
ADD COMMENTlink written 4 weeks ago by lucatucciarone50

Where are you getting your pathways from?

ADD REPLYlink written 4 weeks ago by jared.andrews073.4k

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

ADD REPLYlink written 4 weeks ago by lucatucciarone50

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.

ADD REPLYlink written 4 weeks ago by jared.andrews073.4k

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 : )

ADD REPLYlink written 4 weeks ago by lucatucciarone50

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

ADD REPLYlink written 29 days ago by jared.andrews073.4k

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

ADD REPLYlink written 29 days ago by lucatucciarone50
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