[Feedback] Site Feedback: comparative data across different species

[Sanzhen Liu]

Dear Marcela,

Thank your very much for the information. Is it possible to download or request a file containing orthologs of Zea mays genes? That would be very helpful for our genome-wide studies.

-Sanzhen

On Oct 10, 2014, at 12:29 PM, Marcela K. Monaco <mmonaco at cshl.edu> wrote:

> Dear Sanzhen,
> 
> You may obtain a list of orthologues (or paralogues) for any gene from its Gene Summary page, for example see http://ensembl.gramene.org/Zea_mays/Gene/Summary?db=core;g=GRMZM2G469469;r=2:234351781-234357920;t=GRMZM2G469469_T01
> 
> Note: To get to the Gene Summary page, I simply entered the gene name ("bt1") in the Gramene search box and clicked on the result and selected "zea mays" as species as shown in http://tools.gramene.org/search?query=bt1&fq=species~zea_mays
> 
> If you click on the "Ortologues" (n=47) link or the "Paralogues" (n=8) on the left navigation bar of the Gene page, a table including orthologues for the bt1 gene will appear on your browser and this can be easily downloaded by clicking on the "Excel" icon onthe top right corner of the table. 
> 
> Alternatively, you may get a list of orthologues for a list of genes in certain species by using the customizable Gramene Mart platform, see http://ensembl.gramene.org/biomart/martview as follows:
> 
> 1. Select "Plant Genes (42)" and the dataset of interest, [Zea mays genes (AGPv3 (5b))] in this case. 
> 2. Under "Filters", select "Gene"
> 3. Copy or upload a gene or a list of gene IDS in the "ID list limit" filter
> 4. Under "Attributes", select "Homologs" and then the species for which you want homologs under "Orthologs" or "Paralogs" (Other options such as % identity are available under "Gene"
> 
> Please let us know if we can be of further assistance.  Thanks!
> 
> Marcela
> 
> 
> 
> 
> On Tue, Oct 7, 2014 at 5:58 PM, feedback at gramene.org <feedback at gramene.org> wrote:
> URL         : http://www.gramene.org/ftp-download
> 
> Subject     : Site Feedback: comparative data across different species
> 
> Name        : Sanzhen Liu
> 
> Email       : liu3zhen at ksu.edu
> 
> Organization: Kansas State University
> 
> Comments    :
> 
> Dear sir/madam,
> 
> I spent much time to look for a table containing ortholog information across species. Could you guide me to find that data in your database. Appreciate your help.
> 
> Thanks,
> 
> -Sanzhen
> 
> http://www.warelab.org/bugs/view.php?id=5044
> 
> 
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> 

------
Sanzhen Liu, PhD
Assistant Professor
4022B Throckmorton Plant Sciences Center
Kansas State University
Manhattan, KS 66506-5502
phone: 785-532-1379
fax: 785-532-5692
email: liu3zhen at ksu.edu
twitter: liu3zhen
www.plantpath.ksu.edu/

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