KEGG enrichment for non-model organism

Question

[fanimata]

Hello! I have to do a KEGG enrichment analysis for a non-model organism and already have my KEGG annotations. I know it could be through a Fisher exact test assuming a hypergeometric distribution, but I have no idea how to do it, I just know how to build a contingency table and apply the Fisher test with the formula in R for that. I would like to know if there is a tutorial that can be used as a guide for the analysis. I'm really new in bioinformatics so I don't know much about programming, I barely learning.

Thanks for your help!

[analyst]

Hi Fanimata! How did you get your KEGG annotations for non-model organism? I need to perform KEGG Pathway analysis for non-model organism but i don't have KEGG annotations.

Answer 1

[jared.andrews07]

This question is asked pretty frequently. The enrichKEGG function in the clusterProfiler R package typically works well. See this thread for some additional details. It sounds like you already have what you need to use it.

[fanimata]

Thank you so much, I didn't saw that post! I will try it! :)