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

Peifen Zhang via arab-gen%40net.bio.net (by peifenz from acoma.stanford.edu)
Tue Jun 16 15:20:23 EST 2009

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, 

Please write back to us (curator from plantcyc.org) for any questions using 


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
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