What's the difference between Bioconductor's knownGene and ensGene annotation packages?

Question

[biohack92]

I'm trying to map genomic coordinates for a list of genes to specific features (promoters), but I've come across to different libraries. TxDb.homosapiens.UCSC.hg19.knownGene and TxDb.homosapiens.UCSC.hg19.ensGene. Which library is the right one to use, and what is the difference between the two?

Answer 1

[WouterDeCoster]

There is no right or wrong reference set. ensGene is maintained by ensembl, knownGene by UCSC. They will not be equal. You either make a choice (I have a preference for Ensembl but would like to hear more opinions) or you may want to try to use both to be the most complete.