Question: Plant KEGG pathway analysis in edgeR
0
gravatar for berge2015
3.1 years ago by
berge201590
berge201590 wrote:

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 • 1.8k views
ADD COMMENTlink modified 3.1 years ago by EagleEye6.6k • written 3.1 years ago by berge201590

Which plant are you working on?

ADD REPLYlink written 3.1 years ago by EagleEye6.6k

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

ADD REPLYlink written 3.1 years ago by berge201590

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

ADD REPLYlink written 3.1 years ago by EagleEye6.6k

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

ADD REPLYlink written 3.1 years ago by theobroma221.1k

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

ADD REPLYlink written 21 months ago by lipingchuan0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1105 users visited in the last hour