We calculated the functional group over-representations separately for each functional group dataset. These datasets included 21 COG categories, 168 KEGG categories, 749 metabolic pathways, and 7 additional Mycobacteria-specific groupings (PE genes, PPE genes, toxinantitoxin genes, DosR regulon, esx genes, Rv0474 regulon, and the KstR regulon). We multiplied the hypergeometric p-values by a Bonferroni correction equal to the number of categories or tests performed.