Retrieving chromosomal loci from list of genes?

[Nolte,Mark]

To whom it may concern,

I have an Excel file that has a list of genes with accompanying identifiers, such as: MGI gene symbol, UCSC transcript id and Entrez Gene accession number. However, the table does not contain the chromosomal location of each gene. I'd like to know if there is a way to feed in the complete set of identifiers and get a return file that shows where each gene is located on the mouse genome, build mm9. This would save me a lot of time; otherwise, I would have to go in and enter each gene into the genome browser and make a note of its coordinates.

Any suggestions would be greatly appreciated, sincerely,

Mark Nolte

Graduate Research Assistant

Richard Behringer Lab

University of Texas MD Anderson Cancer Center

713-834-6326

[Brian Lee]

Dear Mark,

Thank you for using the UCSC Genome Browser and your question about
obtaining chromosomal location of genes from unique identifiers such
as UCSC transcripts and Entrez Gene accession numbers.

You can use our Table Browser "identifiers (names/accessions):"
function to upload a list of genes and select the desired output from
the corresponding track. For example, you can pull the coordinates
from the UCSC genes knownGene table if you upload a file of UCSC gene
names similar to this:
uc007aet.1
uc007aeu.1
uc007aev.1
...

1. Navigate to the Table Browser Tool,
http://genome.ucsc.edu/cgi-bin/hgTables, and make the following
selections:

Clade: Mammal
Genome: Mouse
Assembly: mm9
Group: Genes and Gene Prediction Tracks
Track: UCSC Genes
Table: knownGene
Region: genome

2. Click the "upload list" button to use your UCSC genes identifiers
file in the format described above.

3. Set "output format:" to "selected fields from primary and related
tables" and click "get output".

4. On the "Select Fields from mm9.knownGene" page, select your desired
information. For example you can select "name", "chrom", "txStart",
and "txEnd" and then click "get output" to get information similar to
this:

#name chrom txStart txEnd
uc007aet.1 chr1 3195984 3205713
uc007aeu.1 chr1 3204562 3661579
uc007aev.1 chr1 3638391 3648985
...

If you have Entrez Gene identifiers of the type like "382301", which
corresponds to UCSC identifier "uc009vfk.1", you can get the same
output using the Table Browser "filter" tool.

1. Repeat step 1 above.

2. Click the "clear list" button to remove the previous identifier
operation. Next to "filter:", click the "create" button.

3. Scroll down to the "Linked Tables" section and put a check mark
next to the "knownToLocusLink" table and click the "allow filtering
using fields in checked tables" button.

4. Under "mm9.knownToLocusLink based filters", find the "values does
match" line. Replace the "*", with a list of your Entrez Gene
identifiers, for example paste, "18019 11735 11496 16709 12916 ..."
The box is small, but it will accept a list of identifiers.

5. Repeat step 3 from above.

6. Repeat step 4 from above. Here you could use the "Linked Tables" to
add the "value" from knownToLocusLink in your output and you will get
output like:
#mm9.knownGene.name mm9.knownGene.chrom mm9.knownGene.txStart
mm9.knownGene.txEnd mm9.knownToLocusLink.value
uc008oav.1 chr2 168301909 168415848 18019

When selecting a table to browse in the Table Browser, by clicking the
"describe table schema" button you can learn more about other tables.
For example you can also change the above examples Table Browser
settings to "Track: RefSeq Genes" and "Table: RefGene", if you are
using identifiers like "NM_001195025". Or you can make similar filter
selections using Linked Tables based on RefSeq's RefGene table rather
than UCSC knownGene to obtain RefSeq coordinate output. For example
linking through "knownToRefSeq" and then "knownToLocusLink" you can
filter on Entrez Gene IDs and select output like:
#mm9.refGene.name mm9.refGene.chrom mm9.refGene.txStart
mm9.refGene.txEnd mm9.knownToLocusLink.value
NM_010899 chr2 168301909 168415783 18019

Unfortunately it looks like we do not have any track or tables that
contain MGI identifiers of the type "MGI:1341105"

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have further questions please feel free to contact the mailing
list again at gen...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genome Bioinformatics Group

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