KEGGgraph: any way to obtain 'outcome' nodes?
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Paul Shannon ★ 1.1k
@paul-shannon-578
Last seen 8.1 years ago
I have been very happy with the KEGGgraph package, and the easy access to KEGG pathways -- rendered as bioc graphs -- it provides. But now, alas, I am getting greedy... Let me use the human apoptosis pathway as an example. Take a look, please, at http://www.genome.jp/kegg/pathway/hsa/hsa04210.html Many of the signaling paths terminate in biological outcomes, or in other pathways. Dephosphorylation of Bad, for instance, leads to its activation, which leads to apoptosis; this state is displayed on the KEGG page as an unbordered text node labeled 'Apoptosis'. On the other hand, phosphorylation inhibits BAD, and leads to an unbordered text node labeled 'Survival/. As best I can tell, the KEGG xml files do not mention these outcome nodes. Perhaps they only exist in hand curated form, in the png images displayed on the website. Before I manually add outcome nodes to my own curated and evolving version of the graphNEL produced by parseKGML2Graph, I want to ask: has this problem been faced by anyone else? Does anyone have a procedure for creating graphNELs which capture all of the nodes and edges seen at http://www.genome.jp/kegg/pathway/hsa/hsa04210.html? Many thanks, - Paul
Pathways KEGGgraph Pathways KEGGgraph • 1.0k views
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Fraser Sim ▴ 270
@fraser-sim-3567
Last seen 8.1 years ago
Hi Paul, I believe that you're absolutely correct that the KGML does not contain all of the KEGG 'nodes' and some are hard coded into the PNG files. This would prevent any automated approach to adding them into your graph objects. I think the manual approach is the only one which will work in the this case. Hopefully, someone else has found an automated solution as I'd like to take advantage of the same for my own analyses. Cheers, Fraser -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Paul Shannon Sent: Thursday, December 17, 2009 1:37 PM To: bioc Subject: [BioC] KEGGgraph: any way to obtain 'outcome' nodes? I have been very happy with the KEGGgraph package, and the easy access to KEGG pathways -- rendered as bioc graphs -- it provides. But now, alas, I am getting greedy... Let me use the human apoptosis pathway as an example. Take a look, please, at http://www.genome.jp/kegg/pathway/hsa/hsa04210.html Many of the signaling paths terminate in biological outcomes, or in other pathways. Dephosphorylation of Bad, for instance, leads to its activation, which leads to apoptosis; this state is displayed on the KEGG page as an unbordered text node labeled 'Apoptosis'. On the other hand, phosphorylation inhibits BAD, and leads to an unbordered text node labeled 'Survival/. As best I can tell, the KEGG xml files do not mention these outcome nodes. Perhaps they only exist in hand curated form, in the png images displayed on the website. Before I manually add outcome nodes to my own curated and evolving version of the graphNEL produced by parseKGML2Graph, I want to ask: has this problem been faced by anyone else? Does anyone have a procedure for creating graphNELs which capture all of the nodes and edges seen at http://www.genome.jp/kegg/pathway/hsa/hsa04210.html? Many thanks, - Paul _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Paul and Fraser, Thanks for your comments and suggestion! I also believe that KEGG writes lots of information in the PNG file, which cannot be parsed from KGML files. I had heard in a conference sometime ago that in the coming version of KGML this will change, but for now I am not aware of such an approach and would be thankful if anybody could suggest a solution. Nice holidays, David 2009/12/17 Fraser Sim <fjsim@buffalo.edu> > Hi Paul, > > I believe that you're absolutely correct that the KGML does not contain all > of the KEGG 'nodes' and some are hard coded into the PNG files. This would > prevent any automated approach to adding them into your graph objects. I > think the manual approach is the only one which will work in the this case. > Hopefully, someone else has found an automated solution as I'd like to take > advantage of the same for my own analyses. > > Cheers, > Fraser > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Paul Shannon > Sent: Thursday, December 17, 2009 1:37 PM > To: bioc > Subject: [BioC] KEGGgraph: any way to obtain 'outcome' nodes? > > I have been very happy with the KEGGgraph package, and the easy access to > KEGG pathways -- rendered as bioc graphs -- it provides. > > But now, alas, I am getting greedy... > > Let me use the human apoptosis pathway as an example. Take a look, please, > at http://www.genome.jp/kegg/pathway/hsa/hsa04210.html > > Many of the signaling paths terminate in biological outcomes, or in other > pathways. Dephosphorylation of Bad, for instance, leads to its activation, > which leads to apoptosis; this state is displayed on the KEGG page as an > unbordered text node labeled 'Apoptosis'. On the other hand, > phosphorylation inhibits BAD, and leads to an unbordered text node labeled > 'Survival/. > > As best I can tell, the KEGG xml files do not mention these outcome nodes. > Perhaps they only exist in hand curated form, in the png images displayed > on > the website. > > Before I manually add outcome nodes to my own curated and evolving version > of the graphNEL produced by parseKGML2Graph, I want to ask: has this > problem > been faced by anyone else? Does anyone have a procedure for creating > graphNELs which capture all of the nodes and edges seen at > http://www.genome.jp/kegg/pathway/hsa/hsa04210.html? > > Many thanks, > > - Paul > _______________________________________________ > 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 > > _______________________________________________ > 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]]
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