Question

How to use topGO and KEGG with de-novo species

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mictadlo ▴ 10

@mictadlo-10885

Last seen 5.8 years ago

Hi,

According to this side only the following species are supported for topGO and KEGG:

	org.Ag.eg.db	Anopheles
	org.Bt.eg.db	Bovine
	org.Ce.eg.db	Worm
	org.Cf.eg.db	Canine
	org.Dm.eg.db	Fly
	org.Dr.eg.db	Zebrafish
	org.EcK12.eg.db	E coli strain K12
	org.EcSakai.eg.db	E coli strain Sakai
	org.Gg.eg.db	Chicken
	org.Hs.eg.db	Human
	org.Mm.eg.db	Mouse
	org.Mmu.eg.db	Rhesus
	org.Pt.eg.db	Chimp
	org.Rn.eg.db	Rat
	org.Ss.eg.db	Pig
	org.Xl.eg.db	Xenopus

How is possible to use topGO and KEGG with de-novo species?

Thank you in advance

topgo edger limma kegga kegg • 3.4k views

ADD COMMENT • link updated 8.2 years ago by Gordon Smyth 53k • written 8.2 years ago by mictadlo ▴ 10

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topGO can be used with other organism if you provide your own mapping from gene to GO, see the vignette and the documentation

ADD REPLY • link 8.2 years ago Lluís Revilla Sancho ▴ 760

score 0 · Answer 1 · 2017-09-06

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Gordon Smyth 53k

@gordon-smyth

Last seen 1 day ago

WEHI, Melbourne, Australia

Yes, you can use kegga() with your own customized annotation, see: how to use "non-standard" species for KEGG / GO analysis in limma?

This allows you to do use kegga() and topKEGG() to do any analysis, including KEGG or GO analyses of a new species.

Of course you have to be able to supply gene annotation for your species. You can do this by creating an annotation database using annotationHub() or by supplying the gene.pathway data.frame directly.

ADD COMMENT • link 8.2 years ago Gordon Smyth 53k

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Are there any examples how to

creating an annotation database using the gene.pathway data.frame or
creating an annotation database using annotationHub()?

ADD REPLY • link 8.2 years ago mictadlo ▴ 10

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The gene.pathway data.frame is made from the database rather than the other way around: if you already have the data.frame, then you don't need to the database at all. But I've never done it as I don't work with non-model organisms. You might do best to ask a separate question asking people how to do that.

ADD REPLY • link 8.2 years ago Gordon Smyth 53k

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Does my new question how to build gene.pathway data.frame for non-model organism make sense?

ADD REPLY • link 8.2 years ago mictadlo ▴ 10