Dear All,

I have a list from gene and annotation file of Medicago truncatula v4 from phytozome. In this example file, they already provide a list of GO-term and kegg pathway. I would like to ask your suggestion about the program that we can use for go-and pathway enrichment with statistical analysis.

Thanks in advance for your help.

Best regards, Yosapol

It depends on several things. All else equal I would use goseq to do the testing, as you can account for gene length differences which is important. You need the average transcript length and a data.frame with the whatever ID you use in one column and the GO IDs in the next column (so you would have to manipulate that example file because you don't want a comma separated list of GO IDs, but instead want them in individual rows, which means you need repeats of the IDs that the GO IDs map to). There is a User's Manual you can read.