[Arabidopsis] visualizing pathways from list of AtXg numbers

Nicolas Tsesmetzis via arab-gen%40net.bio.net (by nicolas.tsesmetzis from bbsrc.ac.uk)
Fri Aug 10 04:48:39 EST 2007


Hi Dave,
You can use the Arabidopsis Reactome (www.arabidopsis.reactome.org)  
which contains arabidopsis pathways some of which are manually  
curated and the remaining are imported from KEGG and AraCyc. To  
visualize the pathways from your AGI list follow the link to  
"Skypainter" located on the top of the Arabidopsis Reactome home- 
page, paste your AGI identifiers and click "Paint!". A few seconds  
later you should have the corresponded reactions highlighted on the  
reaction map. If your AGI's are followed by normalised expression  
data, Skypainter's coloring will be done according to the average of  
the numeric values of all identifiers linked to the reaction. A time  
series can be displayed as an animation by providing multiple values  
(on the same line, separated by a single space or tab) for each  
identifier.
Please note that this is a pre-release of Arabidopsis Reactome. The  
main release (available in a couple of weeks) contains more  
arabidopsis reactions as well as inferred reactions on other plant  
species through orthologous mapping.
Hope that helps.
Regards,
Nicolas



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