[Genome] Entrez gene ID linked mapping positions for mm8

[Archana Thakkapallayil]

Hello Gwenn,

You could extract this information using the Table Browser, from the 
tables 'knownGene and knownToLocusLink' on the mm8 assembly. To do this, 
click on the "Tables" link in the blue bar at the top of the Genome 
Browser page.  Then make the following selections:

clade: Vertebrate
genome: Mouse
assembly: Feb 2006
group: Genes and Gene Prediction Tracks
track: Known Genes
table: knownGene
region: select the "genome" radio button
output format: choose "selected fields from primary and related tables"
output file: enter a file name here if you wish to save the information 
directly to a file, or leave this blank to view the results in the 
browser window.

click "get output"

On the "Select Fields" page, scroll down to the Linked Tables section 
and check the  'knownToLocusLink' table and then click 'Allow Selection 
 From Checked Tables' button at the bottom of the page. This will allow 
you to pull fields from the tables, knownGene and the knownToLocusLink. 
Check the boxes 'chrom', 'txStart' and 'txEnd' from the knownGene table 
and 'value' from knownToLocusLink table and then click "get output".

The value field of the knownToLocusLink table is the LocusLink ID, now 
known as Gene ID of Entrez.

I hope that this is helpful to you. Please let us know if you have 
further questions.

Regards,

Archana
UCSC Genome Bioinformatics Group



Hansen, Gwenn wrote:
> I am looking for a file for download that would contain the following
> information for refseqs, mRNAs, and/or known genes mapped on the mm8
> assembly:
>  
> Entrez gene ID
> chromosome
> genome start/stop 
>  
> Do you have such a download, or can it be built from available
> downloads?
>  
> Thanks,
> Gwenn
>  
>
>
>
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