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Question: How to use topGO and KEGG with de-novo species
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gravatar for mictadlo
9 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

 

ADD COMMENTlink modified 9 months ago by Gordon Smyth33k • written 9 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 9 months ago by Lluís R330
0
gravatar for Gordon Smyth
9 months ago by
Gordon Smyth33k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth33k 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 9 months ago • written 9 months ago by Gordon Smyth33k

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 9 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 9 months ago by Gordon Smyth33k

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

ADD REPLYlink modified 9 months ago • written 9 months ago by mictadlo0
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