Anyone did the GO term enrichment analysis for the non-model organism or plants Differentially expressed genes recently? I tried to use the agriGOv2 analysis toolkit to get the GO term but couldn't access it. Is it down permanently? ShinyGO is another option but the genes need to be in a specific format like panther, ensemble etc. Could you suggest a better option of doing the analysis in R or using other software?
Hi Afsana,
I recenly performed a GO analysis in a non-model species with DE genes from a DESeq2 analysis. I used the free version of the sowtware Blast2GO. This free version is slow, but works fine. They also have a more complete payment version.
Take a look
https://www.blast2go.com/
I also did a KEGG pathway enrichment analysis useing KOBAS
http://kobas.cbi.pku.edu.cn/
Hope this helps.
Thank you Reza Shokri Gharelo
and Jesús María Vielba for your suggestions. I came up with the goseq R package for the GO term analysis, for which I aligned my reads with a new version of the reference genome from the Ensemble Plants.- Badges
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