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/bioinformatics.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
> >>
> >
> >
> >
>
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