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

Eve Wurtele via arab-gen%40net.bio.net (by evewurtele from gmail.com)
Tue Oct 7 10:12:40 EST 2008


Hi Jianling,

Expanding on this idea, MetaOmGraph (metnetdb.org) enables you to do
correlations with very large datasets (thousands of chips) on either
already-created files of data from Arabidopsis or several other organisms,
or on your own microarray or metabolomic data files.  Alternately, you can
create files from ArrayExpress public microarray data.

There are multiple options for visualization, ordering, and sorting the
types of experimental conditions you want to include in the correlation.

best,
Eve


On Mon, Oct 6, 2008 at 12:29 PM, Iain Manfield <I.Manfield from leeds.ac.uk>wrote:

> 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/ <http://www.dartmouth.edu/%7Ebglab/>
> Dartmouth College
> Hanover, NH 03755 USA
>
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-- 
Eve Syrkin Wurtele, Professor
Bioinformatics and Computational Biology
Dept Genetics, Development, &  Cell Biology
2624D Howe Hall
Iowa State University, Ames IA 50011, USA
515-294-2023
515-708-3232 (cell)

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