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

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
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updated by ashish ashish • written by mahnazkiani mahnazkiani

2 answers

You can try Agrigo to perform GO enrichment analysis :

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

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written by guillaume.rbt guillaume.rbt

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.

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written by mahnazkiani mahnazkiani

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

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written by guillaume.rbt guillaume.rbt

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

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written by mahnazkiani mahnazkiani

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

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written by bbmisraccb • bbmisraccb

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

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written by ashish ashish

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