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Plant KEGG pathway analysis in edgeR

Hi,

Does anyone know if there is a way to conduct KEGG pathway analysis in edgeR using the Plant database only? Or any other program, for that matter? When I use the kegga function, the results only have human KEGG IDs (hsa*). I however want to use only the information from plant species as I'm working with a plant myself.

I know that a 'manual' method exists: using the KEGG KASS site. But having to export gene list, copy, go through email verification, etc seems not so efficient especially when I want to conduct several analyses.

Thank you for your help.

rna-seq kegg r
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updated by EagleEye EagleEye • written by berge2015 berge2015

Which plant are you working on?

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written by EagleEye EagleEye

Wheat, but I'd like to use multiple plant species for my analysis. Arabidopsis, Rice, Maize, etc.

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written by berge2015 berge2015

You can try GeneSCF (easy to use and can run batch jobs).

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written by EagleEye EagleEye

Do you have the EntrezIDs? Why are you restricted to edgeR?

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written by theobroma22 theobroma22

are you able to comments more if not limited to edgeR by using EntrezID? I was thinking blast my protein dataset to Ath.

• 1 views • link
written by lipingchuan • lipingchuan

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