Hi, just want to know if I have obtained KEGG annotation and mapped to pathway using KEGG mapper (http://www.genome.jp/kegg/mapper.html). Due to my lack of skill in doing the gene set enrichment analysis, I have think of a simpler way but not sure whether it is correct?
I simply tabulate how many genes in the mapped to particular gene set (pathway) for both background (whole transcriptome assembly) and sample (DEGs). And also tabulate total genes annotated for both background (whole transcriptome assembly) and sample (DEGs).
Then I will perform using hypergeometric test tool available online (https://www.geneprof.org/GeneProf/tools/hypergeometric.jsp) for every individual pathway.
Is this the correct way? Any simpler way to do this? Or if I am wrong, please guide me to the correct path.