I am dealing with a list of genes which have been selected from a gene enrichment analysis. In order to see what kind of genes are overrepresented, I ran eggnog-mapper to do an orthology assignment of each gene against a bacterial database (provided in eggnog).
After running eggnog you get a .csv file containing for each gene which is the closest ortholog, and a list of GO, KEGG and COG terms associated.
From there, I would like to do a Fisher-test (also considering Bonferroni correction) to highlight COG categories overrepresented in our dataset compared to our reference genome.
Finally my question: How do you deal with genes assigned to multiple COG categories (same would apply for GO terms). You count +1 to each of the COG categories assigned? Do you just choose one category per gene?