Arabidopsis genes & rice orthologues

[Pankaj Jaiswal]

Dear John,

Please see the comments below and feel free to contact us again for 
further questions.

Pankaj
Gramene curator

Fowler.JohnE at epamail.epa.gov wrote:

> 
> Hello,
> 
> I noticed, while searching through your Gramene database, that there are 
> a number of Arabidopsis genes that are apparently not present at all (eg 
> At1g02790).
> 
> Does this mean that these genes do not have rice orthologs, or that they 
> have not been evaluated in the Ensembl compara pipeline?
> 

I believe you searched on the gene ID 'At1g02790' and we have noticed 
that thsi is not possible right now. The only way you can search this is 
by typing 'At1g02790.1-TIGR'. We will be working on improving the 
searches. The gene info you are interested in (At1g02790) is available 
from 
http://www.gramene.org/Arabidopsis_thaliana/geneview?gene=At1g02790-TIGR-G

> 
> There are other Arabidopsis genes that are present, but do not have rice 
> orthologues predicted - I take it that these HAVE been evaluated, but 
> that either there is no rice ortholog, or it is impossible to predict 
> the ortholog using the Ensembl procedure.

Its' not impossible. HOwever as of now our Compara pipeline used very 
conservative  e-value cutoff for the homology (orthology) analysis at 
1e-10. We suspect that this is accounting for at least 20-30% loss of 
orthology mappings to Arabidopsis set. This needs further analysis on 
our side. The current orthology set has about 50% of the Arabidopsis 
genes have a match in rice, as compared to the 80% reported in the 
IRGSP's nature paper.

The same method was used for creating orthology set between rice, maize 
and Arabidopsis.
> 
> thank you for clearing this up.
> 
> 
> I am also interested in more information on how far along the rice - 
> maize gene orthology comparison is - I have a copy of your latest paper 
> from NAR, but it was unclear to me how exactly the rice - maize 
> comparisons were done.  Can you point me to any help information in the 
> database?  I would be particularly interested to find out whether your 
> database has information that would help define orthology between the 
> maize genes represented on the U. Arizona 70-mer oligo array and rice, 
> and possibly then on to Arabidopsis.
> 

Please find this information at http://www.gramene.org/Zea_mays/


> thanks!
> John
> 
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> John E. Fowler
> Associate Professor, OSU Botany and Plant Pathology Dept.
> On Sabbatical at the EPA Western Ecology Division, Corvallis
> email:  fowler.johne at epamail.epa.gov
> Phone: (541) 754-4866