Any recommendation for pathway analysis of Wheat RNA-seq data?

Question

[mahnazkiani]

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.

Answer 1

[guillaume.rbt]

You can try Agrigo to perform GO enrichment analysis :

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

[mahnazkiani]

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.

[guillaume.rbt]

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

[mahnazkiani]

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

[bbmisraccb]

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

Answer 2

[ashish]

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