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Question: How to use topGO and KEGG with de-novo species
0
gravatar for mictadlo
17 months ago by
mictadlo0
mictadlo0 wrote:

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

 

limma topgo edger kegg kegga • 774 views
ADD COMMENTlink modified 17 months ago by Gordon Smyth36k • written 17 months ago by mictadlo0

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

ADD REPLYlink written 17 months ago by Lluís Revilla Sancho460
Answer: How to use topGO and KEGG with de-novo species
0
gravatar for Gordon Smyth
17 months ago by
Gordon Smyth36k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth36k wrote:

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 COMMENTlink modified 17 months ago • written 17 months ago by Gordon Smyth36k

Are there any examples how to

  • creating an annotation database using the gene.pathway data.frame or
  • creating an annotation database using annotationHub()?
ADD REPLYlink written 17 months ago by mictadlo0

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 REPLYlink written 17 months ago by Gordon Smyth36k

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

ADD REPLYlink modified 17 months ago • written 17 months ago by mictadlo0
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