Question

How to create a customized OrgDb in order to perform kegga analysis?

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baus87 • 0

@baus87-13757

Last seen 6.5 years ago

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

limma kegga orgdb • 2.2k views

ADD COMMENT • link updated 6.8 years ago by Gordon Smyth 51k • written 6.8 years ago by baus87 • 0

score 2 · Accepted Answer · 2018-02-18

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Gordon Smyth 51k

@gordon-smyth

Last seen 16 minutes ago

WEHI, Melbourne, Australia

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 COMMENT • link 6.8 years ago Gordon Smyth 51k

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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 REPLY • link 6.8 years ago baus87 • 0

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

ADD REPLY • link 6.8 years ago baus87 • 0

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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 REPLY • link 6.8 years ago Guido Hooiveld ★ 4.1k

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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 REPLY • link 6.8 years ago baus87 • 0

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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 REPLY • link 6.8 years ago Guido Hooiveld ★ 4.1k