Hi N.O., If you have not already tried already, PMN (http://www.plantcyc.org/) would be quite useful. You should find the required info in AraCyc. However, you may have to create a login and play around a bit to get right details. All the best, Avinash On 12 September 2013 05:58, Pj Dias <pjdias87@gmail.com> wrote: > Hi. N.O. > > In my opinion, the best suitable tool for that objective is a network > exploration software like cytoscape. > > 1) Install cytoscape version 2.8.3, and add the toolbox cySBML. > > 2) Obtain the SBML file for the metabolic reconstruction of the organism > you are studying > > 3) search your metabolite, click in it, and then use the cytoscape option > to select the adjacent nodes of selected node. That will give you the > reactions your metabolites is involved. > > 4) By using again the option select adjacent nodes of selected node, you > will obtain your gene names. > > Regards > > Pj > > > 2013/9/12 n omranian <n_omranian@yahoo.com> > > > > > > > Hi, > > > > I have a question, does anybody know a package in bioconductor or any > tool > > (for Arabidopsis thaliana) that if I give a name of metabolite, I get > all > > the genes (known so far) that involved in the reactions in which my > > specific metabolite is playing a role as substrate or product? > > > > Thanks a lot. > > Best, > > N.O. > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]