refseq ids associated with gene symbols

[Pete Shepard]

Dear UCSC Genome Browser,

I have a list of gene symbols or gene identifiers of some sort, I would like to obtain refseq IDs for each symbol/gene identifier. Using my current approach, I can find a refseq IDs for  >95% of the gene symbols.

For the remaining 5%, I paste the gene symbol into the Genome Browser's search term and this almost always get me the output I want.

My question is, can I  to create a table using the Table Browser that can reproduce what

the search term feature in the Genome Browser is doing?

Thank you

 

[Luvina Guruvadoo]

Hello Pete,

Thanks for your question. Could you please send us a few examples of
the remaining 5% and let us know which approach you are using to
obtain the RefSeq IDs for the other 95%?

If you have any further questions, please reply to
gen...@soe.ucsc.edu. All messages sent to that address are archived on
a publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group

> --
>

[Pete Shepard]

Hi Luvina,

Thanks for getting back to me. The approach I take is to use the Table Browser and select Genes and Gene Predictions Group, the RefSeq Genes Track and the refGene table. I then choose "selected fields from primary and related tables" from the output format option and select the kgXref from the linked tables. I then click on "allow selection from checked tables" and choose kgID, geneSymbol, and refseq from the hg19.kgXref fields.Three of the gene identifiers that do not appear in this list are below. However, I can retrieve a Refseq id if I use these identifiers in the UCSC Genome Browser's search feature.

Thanks again

KIAA0317
BRP44
SFRS2B

[Luvina Guruvadoo]

Hello Pete,

When I paste these 3 identifiers in the Table Browser, I get the
following output:

#hg19.kgXref.kgID hg19.kgXref.geneSymbol hg19.kgXref.refseq
uc001ges.3 MPC2 NM_015415
uc001get.3 MPC2 NM_001143674
uc001geu.3 MPC2 NM_015415
uc001pff.3 SRSF8 NM_032102
uc001xqb.3 AREL1 NM_001039479
uc010tut.1 AREL1 NM_001039479

The gene identifiers for each of these transcripts is listed under the
"Other Names" section on the gene detail page. uc001ges.3, for
example, shows BRP44:
http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc001ges.3&db=hg19#synonym.
This section is populated from kgAlias. To see this in your output,
select hg19.kgAlias from the linked tables section in the Table
Browser (click on "allow selection from checked tables" > select
hg19.kgAlias > click on "allow selection from checked tables" > select
the "alias" field from kg.Alias).

If you have any further questions, please reply to
gen...@soe.ucsc.edu. All messages sent to that address are archived on
a publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group

[Pete Shepard]

Thanks Luvina,

This gets more of my results but not all of them.

I can now find the field that I am looking for in the Genome Browser it is called "Alternate Gene Symbols"  and it is a sub category of "Other Names for This Gene". I can get here by pasting in my gene identifier and clicking on the gene under UCSC Genes track. Can you tell me how I can get Alternate Gene Symbols"  and "Other Names for This Gene" from the Table Browser?

[Steve Heitner]

Hello, Pete.

The kgAlias table that my colleague mentioned is the source of the “Alternate Gene Symbols” list in the “Other Names for This Gene” section.  To verify this, you can directly query the table in our public MySQL server (for instructions, see https://genome.ucsc.edu/goldenPath/help/mysql.html).

For example, for uc001ges.3, you would make the following query:

select * from kgAlias where kgID="uc001ges.3";

If you see it in “Alternate Gene Symbols” on the page, it’s in kgAlias.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  All messages sent to that address are archived on a publicly-accessible Google Groups forum.  If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

---
Steve Heitner
UCSC Genome Bioinformatics Group

--