Question: Any recommendation for pathway analysis of Wheat RNA-seq data?
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gravatar for mahnazkiani
6 weeks ago by
mahnazkiani50
United States
mahnazkiani50 wrote:

I have RNA-seq data for Wheat samples, and have a problem to find a way to do functional analysis such as Pathway analysis, any recommendation appreciated.

rna-seq wheat • 185 views
ADD COMMENTlink modified 6 weeks ago by ashish270 • written 6 weeks ago by mahnazkiani50
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gravatar for guillaume.rbt
6 weeks ago by
guillaume.rbt770
France
guillaume.rbt770 wrote:

You can try Agrigo to perform GO enrichment analysis :

http://systemsbiology.cau.edu.cn/agriGOv2/

ADD COMMENTlink written 6 weeks ago by guillaume.rbt770

Thank you for your response, I did use AgriGo, but none of my DEGs mapped. Do you have any recommendations for pathway analysis? I have used KOBAS before for other species, but they don't have a wheat genome.

ADD REPLYlink written 6 weeks ago by mahnazkiani50

What do you mean by "none of my DEGs mapped" ? Have you been able to run agriGO and found no enriched GO?

ADD REPLYlink written 6 weeks ago by guillaume.rbt770

Yes, I did run the agriGO, and didn't find any enriched GO

ADD REPLYlink written 6 weeks ago by mahnazkiani50
1

And, sure not an ID conversion issue? Strange that AgriGO would not map any plant DEGs for GO analysis.

ADD REPLYlink written 6 weeks ago by bbmisraccb60
0
gravatar for ashish
6 weeks ago by
ashish270
ashish270 wrote:

You can use plant reactome for wheat pathway mapping. The website is currently down for maintenance till 8th december.

ADD COMMENTlink written 6 weeks ago by ashish270
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