Dear all, I am using the KEGGgraph package to construct metabolic networks of various organisms and study their topological properties.My query though is : Can the package KEGGgraph be used to construct a weighted directed graph in which the nodes are the pathways themselves and they are connected if they share enzymes ? The no. of enzymes any two pathways share can be used to give a weight to the edge between the two pathways (nodes in this case). Thanks in advance for any help. Regards, Anupam [[alternative HTML version deleted]]

Hi Anupam, I am the author and the maintainer of the KEGGgraph, and I will try to answer your questions. Although I have never done this before, but I believe the following pipeline should do the job (1) Download the pathway KGML files with retrieveKMGL function or manually from the KEGG FTP server (2) Parse them in a list with parseKGML2Graph (3) use lapply(list, nodes) to list the nodes of each graph (4) Build a NxN matrix, with N equalling to the number of the KGML files. Fill the matrix with the intersecting nodes between each pathway. (5) Convert the matrix into a (undirected) graph Best wishes, David 2009/11/27 anupam sinha <anupam.contact@gmail.com> > Dear all, > I am using the KEGGgraph package to construct metabolic > networks of various organisms and study their topological properties.My > query though is : Can the package KEGGgraph be used to construct a > weighted > directed graph in which the nodes are the pathways themselves and they are > connected if they share enzymes ? The no. of enzymes any two pathways share > can be used to give a weight to the edge between the two pathways (nodes > in > this case). Thanks in advance for any help. > > > > Regards, > > Anupam > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Jitao David Zhang Biological Statistics and Computational Biology Ph.D. Division of Molecular Genome Analysis DKFZ, Heidelberg D-69120, Germany http://www.NextBioMotif.com/ [[alternative HTML version deleted]]