[Genome] How to get gene names in a batch given accession IDs of mRNA or EST?

[Brooke Rhead]

Hello Long,

The association of mRNA and EST IDs with gene names does not exist in 
any of our tables.  You could instead use the Table Browser to create 
custom tracks from the all_mrna and all_est IDs and then intersect the 
custom tracks with one of the gene tracks to get the corresponding gene 
names.  However, the Table Browser does not have a "join" function that 
will give you the mRNA/EST name in the same table as the gene name (it 
will only return a list of the gene names that intersected with your 
custom tracks -- you will not be able to tell which mRNA/EST goes with 
which gene).

There is another tool run by Penn State that works in conjunction with 
the UCSC Genome Browser that can do joins.  It is called "Galaxy", and 
it is located here:

http://main.g2.bx.psu.edu/

Galaxy has a tool to "Join the intervals of two queries side-by-side" 
that you can use to join the intervals of your specific mRNAs or ESTs 
with the intervals of a gene track, from which you can get a gene name, 
or at least a gene accession.  (If you are working with hg18, I 
recommend using the "RefSeq Genes" track, which has a gene common name 
in the 'name2' field.)

Some notes about using Galaxy:

- You can access the UCSC Table Browser through the "UCSC Main table 
browser" link on the left-hand side under "Get Data".  Note that Galaxy 
defaults to May 2004 (hg17), which is not our most recent human build.

- The "join intervals" function is under the "Operate on genomic 
intervals" section on the left-hand side.

- Galaxy has a wiki page available on interval operations:
http://g2.trac.bx.psu.edu/wiki/GopsDesc

I hope this information is helpful.  If you have further questions for 
us, please do not hesitate to contact us again.  If you have questions 
about Galaxy, please contact their help desk at galaxy-user at bx.psu.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Long Li wrote:
> Hi,
> 
> I have a lot of IDs of mRNA (from all_mrna table) and EST (from all_est
> table), my question is how to get their gene names in a batch.
> 
> For example, the DA561869 and AL602556 are from all_est table, the
> AK074693 is from all_mrna table.  But they are belong to gene CABC1.  So
> which table should I look up to find the gene name CABC1?  Thanks.
> 
> Long
> 
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