[Genome] Gene symbol in table browser

[Rachel Harte]

Hi Chen,

You can do this in the Table Browser if you use the RefSeq track and
follow these steps:

1) Select the genome and assembly.
2) Select "Genes and Gene Predicton Tracks" as the group and RefSeq Genes
as the track.
3) Select refFlat as the table and region: genome
4) Then you can use the buttons by the identifiers (names/accessions) to
paste a list of gene symbols or upload a list of gene symbols.
5) Choose your output.

If you would like to use the Known Genes track, it is not possible at the
moment to search it directly with identifiers. You would need to use
the Table Browser and select the Known Genes track and the kgXref
tabl and search with the list of gene symbols as above and get the
list of accessions for these gene symbols as output. Then repeat the steps
above for the knownGene table but paste in a list of accessions.

Please bear in mind, that the RefSeq track is updated frequently to keep
in step with GenBank updates while, currently, Known Genes is not updated.

I hope that this helps you. Please let us know if you have further
questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


> Subject:
> Gene symbol in table browser
> From:
> Chen Su <SU_CHEN at LILLY.COM>
> Date:
> Fri, 23 Mar 2007 10:29:10 -0400
> To:
> genome at soe.ucsc.edu
>
> To:
> genome at soe.ucsc.edu
>
>
>
> Hi,
> I have a list of ~100 official human gene symbols that I'd like to use
> as query and get have the chromosomal locations in a BED file. Can I use
> Table Browser to do that? If not, what else can I use?
> Thank you in advance!
> - Chen
>
> I attached some examples here:
>