Hello Fenglei He,
You can convert your UCSC identifiers using the table browser
(http://genome.ucsc.edu/cgi-bin/hgTables).
After selecting your assembly of interest (mm9) select:
group: Genes and Gene Prediction Tracks
track: UCSC Genes
table: kgXref
Then you can either paste in your list of identifiers or upload them as
a text file (in the "identifiers (names/accessions)" section). Then 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 (i.e. gene symbol) 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 10/06/10 11:32, He, Fenglei wrote:
> Dear UCSC bioinformatics experts:
>
>
>
> I just generated a list of genes from RNA-seq experiment. However, all
> the gene id are displayed in a format of like this: uc007bbm.1
>
>
>
> In my RNA-seq analysis, I have used mm9 genome as reference. How to
> convert these id into gene names?
>
>
>
> Thanks very much
>
>
>
> Fenglei He
>
>
>
> Postdoctoral Fellow
>
> Mount Sinai School of Medicine
>
> Dept. of Developmental and Regenerative Biology
>
> 1468 Madison Avenue, Box 1020
>
> New York, NY 10029-6574
>
> [email protected]
>
> Tel: (212) 241-0937
>
> Fax: (212) 860-9279
>
> http://research.mssm.edu/soriano/lab/
>
>
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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