Question: correct order for pathway analysis
1
gravatar for Sara
7 weeks ago by
Sara130
Sara130 wrote:

I am doing pathway analysis but there a lot of tutorials so, I am looking for the correct way of doing that.

1- I got DE genes (up and down regulated)
2- filter them based on log2 of FC. only the genes with Log2FC > 1 or Log2FC < -1 are used for pathway analysis
3- I used up and down regulated genes together (only gene name) for pathway analysis (using DAVID) to identify up and down regulated pathways.

the question is that, ma I following the correct order? if not what is the correct order and tool?

gene • 130 views
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by Sara130
1

What is your reasoning for combining up/down in 3?

The list of down- and up-regulated genes indicates which genes are being affected by your treatment, the combination of both are representing all pathways that could be affected, but you cannot separate up- from down-regulated pathways.

In my opinion, it's better to perform pathway enrichment separately, with the main hypothesis: if several or key genes are up-regulated and are part of a pathway, the pathway is also up-regulated, similar hypothesis for down-regulated.

ADD REPLYlink written 7 weeks ago by JC11k

I agree with what JC said. Additionally, I recommend using an updated, well-maintained pathway tool such as enrichr: https://maayanlab.cloud/Enrichr/ instead of DAVID.

ADD REPLYlink written 7 weeks ago by dsull1.6k
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