Ucsc: Which Gene Name Annotation Are You Using?

Question

[Maxime Lamontagne]

Hi,

I'm doing a locus zoom and I'm wondering which gene annotation to use. In UCSC, you have UCSC, ENCODE/GENCODE and RefSeq genes. So which ones is the "better".

Thanks

Answer 1

[tayebwajb]

I think it depends on which level you are interested in, i.e., genomic or transcriptome. I would use UCSC known genes for the former and GENCODE for the latter. I prefer to use UCSC known genes. I recently was doing structural variant analysis and I found that the breakpoint I obtained in the STAT6 gene was outside the coordinates of the RefSeq genes but within the STAT6 UCSC known gene. This got me confused at first because I thought that the breakpoint was probably in a region where two contigs overlap in the genome assembly, with no annotation in that region.

Apparently, GENCODE v15 contains the most comprehensive functional annotation for the complete human genome. https://gencodegenes.wordpress.com/2013/05/21/gencode-v15-a-complete-firstpass-manual-annotation-of-the-human-genome/