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.
Jaime Enrique Plazas Román Thank you for the recommendation, I couldn't figure it out though, I have a gene list not the fasta files. appreciate your help.
1. Use the https://www.genome.jp/kegg/ link and paste your gene name and search for the orthologous KEGG pathway. Classify the pathways into main pathways using the link https://www.genome.jp/kegg/pathway.html
It includes the pathway: Complement and coagulation cascades, which belongs to the main pathway: Immune system).
2. Identify the homologous gene sequences in Uniprot and download them in fasta format. Identify the KEGG Pathways using the https://www.kegg.jp/ghostkoala/ or https://www.kegg.jp/blastkoala/.
3. you can use http://kobas.cbi.pku.edu.cn/kobas3/annotate/ and paste the genes to annotate the pathways.
Sayan Paul thank you for information, this is make sense for the gene that you used as an example, but when I am using the wheat gene ids that I have, I don't get any results back. I attached the file with the gene names.