[Genome] Finding human-rat orthologs

[Kayla Smith]

Hello Pierre,

You'll want to use the hg18.mmBlastTab table.  This table connects the 
UCSC Genes ID for human and mouse.  So we'll have to translate to them 
first.

Here is how to get this data in the Table Browser:

clade: Vertebrate
genome: Human
assembly: Mar. 2006
group: All Tables
database: hg18
table: knownToLocusLink
output format:  "selected fields from primary and related tables"
click "get output"

Check the boxes for both the name and value fields in 
hg18.knownToLocusLink, and then scroll down to the Linked Tables section 
and check the box next to hg18.mmBlastTab.  Then click "Allow Selection 
from Checked Tables".  Now check the boxes next to "target" and click 
"get output"

I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group


Bushel, Pierre (NIH/NIEHS) [E] wrote:
> I have a list of human genes with LocusLink IDs and Entrez Gene IDs.  I
> want to obtain rat orthologs for these human genes.  Is there a way to
> do it in batch mode?
> 
>  
> 
> Thanks,
> 
>  
> 
> Pierre R. Bushel, Ph.D.
> 
> Head, Microarray and Genome Informatics
> 
> Staff Scientist, Biostatistics Branch
> 
> National Institute of Environmental Health Sciences
> 
> 111 T.W. Alexander Drive
> 
> P.O. Box 12233
> 
> RTP, NC 27709
> 
> (VM) 919-316-4564
> 
> (Fax) 919-316-4649
> 
> bushel at niehs.nih.gov
> 
>  
> 
> _______________________________________________
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