Question: How to create a customized OrgDb in order to perform kegga analysis?
0
gravatar for baus87
15 months ago by
baus870
baus870 wrote:

Hi,

i'm working on a set of DEGs and i'd like to analyze them using the kegga function. Since i'm working on a species whose OrgDb is not implemented in, how can i create an in-house dedicated OrgDb?
thanks in advance,

Antonio

orgdb limma kegga • 354 views
ADD COMMENTlink modified 15 months ago by Gordon Smyth37k • written 15 months ago by baus870
Answer: How to create a customized OrgDb in order to perform kegga analysis?
2
gravatar for Gordon Smyth
15 months ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

You don't need an OrgDb package to run kegga(). kegga simply reads annotation from the KEGG website.

However KEGG does not provide annotation for the Trichoderma gamsii species, as you can see from their website:

http://www.kegg.jp/kegg/catalog/org_list.html

The closest species is Trichoderma reesei.

So you can't do a KEGG enrichment analysis for Trichoderma gamsii because KEGG pathways don't exist for that species.

ADD COMMENTlink modified 15 months ago • written 15 months ago by Gordon Smyth37k

Dear Gordon,
i'm working with Trichoderma gamsii (filamentous fungus). I'd like to perform a kegg enrichment analysis upon DEGs. Is it kegga suitable for this purpose?

ADD REPLYlink written 15 months ago by baus870

Ok, got it.
Could you recommend me any alternative tool?

ADD REPLYlink written 15 months ago by baus870

Let me ask you in turn: is there any pathway / annotation info publicly available for this organism? At KEGG apparently not... Being a person working with T gamsii I suppose you should know this.... If there isn't, you cannot expect members of this (Bioconductor) support site to give you a useful answer to your last question....

ADD REPLYlink modified 15 months ago • written 15 months ago by Guido Hooiveld2.4k

Dear Guido,
nowadays i'm annotating my reference genomes with ko codes from KEGG. Given a set o differentially expressed genes, I was just looking for the proper enrichment analysis to be applied. Maybe my first post has been misleading, sorry for that.
Antonio

ADD REPLYlink modified 15 months ago • written 15 months ago by baus870
1

Aha, AFAIK in that case you can use the argument species.KEGG = "ko" when using the function kegga().

Assuming DEGs is a character vector with the differentially expressed KO IDs, something like:

k<- kegga(DEGs, species.KEGG = "ko", FDR = 0.05)
ADD REPLYlink written 15 months ago by Guido Hooiveld2.4k
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