KEGGgraph query
1
0
Entering edit mode
anupam sinha ▴ 270
@anupam-sinha-3207
Last seen 8.1 years ago
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]]
Pathways graph KEGGgraph Pathways graph KEGGgraph • 660 views
ADD COMMENT
0
Entering edit mode
@jitao-david-zhang-3188
Last seen 5.7 years ago
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]]
ADD COMMENT

Login before adding your answer.

Traffic: 289 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6