Dear All, Is this package useful to do pathway analysis with RNA-seq based expression data - say for eg. gene expression analysis results from tophat/cuflinks pipeline ? Regards, Krishna Mohan On Fri, Jun 28, 2013 at 4:19 AM, Luo Weijun <luo_weijun@yahoo.com> wrote: > > > A little more info. You > may download the KGML data file for Propanoate metabolism pathway. Gene > nodes > correspond to node entries with type="gene", while white nodes > correspond to entries with type="ortholog", ortholog genes which are > not mapped for a particular KEGG species. > These ortholog gene > nodes are still show are in both KEGG and Graphviz view, except no gene > data > can be mapped when calling pathview function with species = "hsa" (or > other KEGG species). However, gene data can still be mapped to these nodes > when > species = "ko". This is relevant for ortholog gene data or > metagenomic data. > HTH. > > > ----- Original Message ----- > From: Luo Weijun <luo_weijun@yahoo.com> > To: Ed <edforum@gmail.com> > Cc: BioC Help <bioconductor@r-project.org> > Sent: Thursday, June 27, 2013 6:32 PM > Subject: Re: [BioC] Pathview published in Bioinformatics > > Yes, you can replace > get gene symbols instead of EC numbers by setting kegg.native = T, > same.layer = > F for KEGG view. However, only those enzyme nodes/genes which are present > in > the KGML data file. These nodes are marked in green in original KEGG graph > for > particular species, for example Propanoate > metabolism - Homo sapiens: > http://www.genome.jp/kegg-bin/show_pathway?map=hsa00640 > In fact for Graphviz > view (kegg.native = F), the pathway graph are also limited to genes which > are > presented in KGML data file. Hence you may see some inconsistence for > metabolic > pathway graphs between KEGG view and Graphviz view. Unfortunately, there is > little we are limited by the KGML source data files. > > > ________________________________ > From: Ed <edforum@gmail.com> > To: Luo Weijun <luo_weijun@yahoo.com> > Sent: Thursday, June 27, 2013 12:04 AM > Subject: Re: [BioC] Pathview published in Bioinformatics > > > > so if I understand and tried correctly, > > I cannot simply replace the EC in the graph (like Propanoate metabolism) > with gene symbol. If I need to do so, I need to set kegg.native=F, which > means it will change the graph structure of Propanoate Metoblism. Am I > right? > > > > On Wed, Jun 26, 2013 at 1:03 PM, Luo Weijun <luo_weijun@yahoo.com> wrote: > > Hi Nick, > >Yes, you can get > gene symbol instead of EC (or original KEGG node labels). If you want a > native KEGG view, set kegg.native > = T, same.layer = F when you call pathview function. Otherwise, simply set > set kegg.native > = F for a Graphviz view. As example outputs, you may compare the gene > symbols > in Figure 1b and Figure 2 vs Figure 1a in the vignette. HTH.Weijun > > > > > >________________________________ > > From: Ed <edforum@gmail.com> > >To: Luo Weijun <luo_weijun@yahoo.com> > >Sent: Tuesday, June 25, 2013 9:10 PM > >Subject: Re: [BioC] Pathview published in Bioinformatics > > > > > > > >Hi Dr. Luo, > > > > > >It is a really good job! > > > > > >I am just wondering if you can change the EC into gene symbol for the > enzyme in KEGG pathway? > > > > > >Thanks, > > > > > >Nick > > > > > > > > > > > > > > > >On Tue, Jun 25, 2013 at 8:14 PM, Luo Weijun <luo_weijun@yahoo.com> wrote: > > > >BioC List, > >>The pathview package was recently published in > >>Bioinformatics: > >> > http://bioinformatics.oxfordjournals.org/content/early/2013/06/11/bi oinformatics.btt285.full > >> > >>Pathview is an R/Bioconductor package for pathway based data > >>integration and visualization. It maps and renders a wide variety of > biological > >>data on relevant pathway graphs. > >> > >>The package is available through Bioconductor and R-Forge: > >>http://bioconductor.org/packages/release/bioc/html/pathview.html > >>http://pathview.r-forge.r-project.org/ > >>Please try it out and let me know if you have any > >>comments/suggestions. Thank you! > >>Weijun Luo > >> > >> > >>_______________________________________________ > >>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 > >> > > > > > > > > _______________________________________________ > 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]]