Re: [Arabidopsis] How to identify a specific metabolic pathway from a list of genes.

[Peifen Zhang]

Hi Kumar,

Have you tried the "Omics Viewers" tool from AraCyc,
http://www.plantcyc.org:1555/ARA/expression.html. The tool is ideal for
displaying quantitative large-scale omics data, such as gene expression,
on Arabidopsis metabolic pathways. For example, reaction steps of
pathways will be color-coded with up or down- regulated enzyme-coding
genes. It allows you visualize and quickly spot areas of metabolism
responding to a particular experimental condition. A tutorial on the
tool is at http://www.plantcyc.org/tutorials/omics_viewer_tutorial.faces.

You can also use the tool to display a list of genes without
quantitative data, by simply making up/providing any data value (i.e 2)
for all the genes on your input file.

There is also a flat file of AraCyc that you can use to look up
pair-wise info about genes and pathways,
ftp://ftp.arabidopsis.org/home/tair/Pathways/aracyc_dump.20090311.

Please write back to us (cur...@plantcyc.org) for any questions using
AraCyc.

Regards,
Peifen

KKB wrote:
> Hi,
> I have a list of Arabidopsis genes identified from microarray studies. I
> want to find out if these genes are part of any specific metabolic
> pathways. I have been exploring AraCyc of TAIR, but I am not able find a
> platform where I can input any genes that will tell me the related
> pathway. I will really appreciate if you have a suggestion on how to
> find if any of these genes are involved in or are regulating any
> specific metabolic pathways.
>
> Thanks,
> Kumar
>
> _______________________________________________
> Arab-gen mailing list
> Arab...@net.bio.net
> http://www.bio.net/biomail/listinfo/arab-gen

[Eve Wurtele]

Hi Kumar,

Go to AtGeneSearch at MetNet metnetdb.org

Paste in your gene list, you will get a table with info about pathways, GO
terms, regulons membership and more for each gene, plus clickable links to
more info.

Of course, for the many Arabidopsis genes of unknown function, there will be
no pathway listed.

best,
Eve

On Tue, Jun 16, 2009 at 1:04 AM, KKB <kik...@gmail.com> wrote:

> Hi,
> I have a list of Arabidopsis genes identified from microarray studies. I
> want to find out if these genes are part of any specific metabolic pathways.
> I have been exploring AraCyc of TAIR, but I am not able find a platform
> where I can input any genes that will tell me the related pathway. I will
> really appreciate if you have a suggestion on how to find if any of these
> genes are involved in or are regulating any specific metabolic pathways.
>
> Thanks,
> Kumar
>
> _______________________________________________
> Arab-gen mailing list
> Arab...@net.bio.net
> http://www.bio.net/biomail/listinfo/arab-gen
>

--
Eve Syrkin Wurtele, Professor
Bioinformatics and Computational Biology
2624D Howe Hall, VRAC, Iowa State University,
Ames IA 50011, USA
515-708-3232 (cell)
https://www.metnetdb.org
https://www.metablast.org

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