[Genome] Finding human-rat orthologs

[Donna Karolchik]

A small typo in Kayla's email -- I believe she meant to say
rnBlastTab (rat) rather than mmBlastTab (mouse).

-Donna

----- Original Message ----- 
From: "Kayla Smith" <kayla at soe.ucsc.edu>
To: "Bushel, Pierre (NIH/NIEHS) [E]" <bushel at niehs.nih.gov>
Cc: <genome at soe.ucsc.edu>
Sent: Thursday, January 17, 2008 3:49 PM
Subject: Re: [Genome] Finding human-rat orthologs


>
> 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
>>
>>
>>
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>