[Arabidopsis] How to identify a specific metabolic pathway from
a list of genes.
(by peifenz from acoma.stanford.edu)
Tue Jun 16 15:20:23 EST 2009
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
> 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.
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