topGO enrichment: Should the "Gene universe" also contain genes with no GO term?
I have a set of interesting genes with GO terms, I want to find out which GO terms are enriched compared to a background set (gene universe).
My gene universe is all the genes that showed evidence of expression in my genome. However, not all of those genes (expectedly) had GO terms (Retrieved from eggNOG) associated with them. Should I still include them in my gene universe but with "nan" as it's associated GO term or only use genes that have a GO term?
Thank you in advance!
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