Link pathways to Gene Onthologies from RNA-seq differential expressed genes
0
0
Entering edit mode
3.2 years ago

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 • 516 views
ADD COMMENT
0
Entering edit mode

Where are you getting your pathways from?

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 850 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6