Hello Jiangning Li,
Unfortunately we do not have any tables which use the Entrez Gene ID as
a primary key. This means that you will have to look up each ID
individually. To do this go to the Table Browser
(http://genome.ucsc.edu/cgi-bin/hgTables)and after selecting your
assembly of interest select:
group: Genes and Gene Prediction Tracks
track: UCSC Genes
table: knownGene
Filter - click "create". Then in the next menu scroll down to the
"Linked Tables" section and check the box beside the knownToLocusLink
table. Then continue scrolling down and click on "Allow Filtering Using
Fields in Checked Tables". This should bring up another menu:
"hg19.knownToLocusLink based filters"
For each of the Entrez Gene IDs that you have paste this into the "value
'does' match [your ID - i.e. 10772]" then click submit.
If you only want to retrieve certain columns from a given table you can
also select:
output format: "selected fields from primary and related tables"
Once you click on "get output" this will take you to a menu where you
can specify which fields you want to retrieve from your tables of
interest.
Hopefully this information was helpful and answers your question. If you
have further questions or require clarification feel free to contact the
mailing list at [email protected].
Regards,
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
On 02/23/11 11:50, Jiangning Li wrote:
> Dear Sir/Madam,
>
>
>
> I am trying to download 2000bp of sequence from the transcription start site
> for a list of genes, I have the unique EntrezGene IDs, how can I do it from
> UCSC genome browser? Previously I got coordinates of each gene, but I found
> various coordinates for the same genes which gave me wrong sequences. It
> will be greatly appreciated if you can give some hints. Thanks.
>
>
>
> Best,
>
>
>
> Jiangning Li
>
>
>
> Institute for Systems Biology
>
> Seattle, WA 98103
>
> 206-732-2168
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
