Hi all,

Can my input list of genes for enrichGO analysis be a list with both- up and downregulated genes?

Thank you!

Yes, it can. Be sure to properly interpret the results; over-represented GO categories could then either be due to the up-regulated or down-regulated genes (or a combination thereof). If you want to deduce whether from a biological perspective a process seems to be more or less active (in the experimental group compared to the reference), you will thus need to check afterwards the (log2) fold changes of the genes belonging to a GO category.