Question: GO enrichment for non-model plant species
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gravatar for sandeep.amberkar18
3 months ago by
Rothamsted Research UK
sandeep.amberkar180 wrote:

Hello,

Has anyone done an enrichment analysis for non-model plant species such as Wheat (Triticum aestivum). As a first step, I generated a gene-GO-GOdescription mapping as fetched from Ensembl Plants, which looks something like this:

              GeneID      GO-ID                                       GO-Description

TraesCS3A02G154800 GO:0047617                          acyl-CoA hydrolase activity
 TraesCS2B02G516800 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
 TraesCS2B02G516800 GO:0005975                       carbohydrate metabolic process
 TraesCS2B02G516800 GO:0016787                                   hydrolase activity
 TraesCS2B02G516800 GO:0016798         hydrolase activity, acting on glycosyl bonds
 TraesCS2B02G516800 GO:0008152                                    metabolic process

I'm trying to generate an MSigDB type gmt file from this table, which can then be used as input for the clusterProfiler function enricher.

I get duplicates found error which is why I can't proceed any further with an enrichment analysis.

Any body has any nifty solution, please do share.

With thanks.

Best, Sandeep

ADD COMMENTlink written 3 months ago by sandeep.amberkar180

How did you create the gmt file? Did you try to create a GeneSetCollection for clusterProfiler (this way you wouldn't need to create a gmt file)?

ADD REPLYlink written 3 months ago by Lluís Revilla Sancho530

No, I didn't create a GeneSetCollection object. How could that be passed to enricher function?

ADD REPLYlink written 3 months ago by sandeep.amberkar180

I think that you can convert it to a list, or it is already accepted, but check the vignette and the manuals

ADD REPLYlink written 3 months ago by Lluís Revilla Sancho530
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