[Arabidopsis] cis element analysis - using co-expressed genes.

[Iain Manfield]

Dear Jianling,

If you're interested in promoters of Arabidopsis genes... we have
developed a site calculating the correlation of expression patterns for
Arabidopsis genes from a database of Affymetrix microarray experiments.
Co-expressed genes are often co-regulated and therefore analysis of a
set of promoters for strongly co-expressed genes (including the promoter
you're most interested in) can help to predict significant motifs with
better confidence than looking at a single sequence. 

http://www.arabidopsis.leeds.ac.uk/act/coexpanalyser.php#CO2

Use the "ID exchanger" to get the Affymetrix probe ID from an AGI code
and put this into the "probe ID" box at the site with the above address.


With a set of AGI codes from the returned list you can get the promoter
sequences from TAIR and use the SCOPE tool as Robert Gross has suggested
(amongst other tools). 

Best wishes,

Iain.

Dr Iain Manfield
Centre for Plant Sciences
Faculty of Biological Sciences
University of Leeds
Leeds
LS2 9JT
U.K.
 
Tel. 00 44 (0)113 343 7279
 
--- You wrote:
Hi,

Is there anybody who can give me some suggestions how to analyze the
cis-
element in the promoter region?

Any suggestions are appreciated.

Thanks!

Jianling
--- end of quote ---
Hello Jianling -

Your note was forwarded to me from a colleague. My lab has developed
something  
to do exactly this called SCOPE. You can access it at:
<http://genie.dartmouth.edu/scope/>.

It is designed to find common regulatory elements for any set of genes
that you  
input to the server. There are references to papers on the genie server.

Please let me know if you have any questions or would like to talk about
your  
questions. I'm always open to new collaborations.

Good luck.

Bob Gross

------------------------------------------------------------------------
-----
Robert H. Gross, Ph.D.                                    phone:
603-646-2059
Assoc. Prof., Dept. Biology               email:
robert.h.gross from dartmouth.edu
Director, Ctr. for Biol. & Biomed. Computing               Office:
Remsen 210
Gilman Labs 104                         URL:
http://www.dartmouth.edu/~bglab/
Dartmouth College
Hanover, NH 03755 USA

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