[BioC] Kegg pathway --> gene network

[Marc Carlson]

Before anyone runs off to write a new package, a new package is being
added to bioconductor right now that looks like it might do some of what
you are looking for:

Package: KEGGgraph
Type: Package
Title: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
Version: 0.8.6
Date: 2008-12-11
Author: Jitao David Zhang and Stefan Wiemann
Maintainer: Jitao David Zhang <j.zhang at dkfz.de>
Description: KEGGGraph is an interface between KEGG pathway and graph
object as well as a collection of tools to analyze, dissect and
visualize these graphs. It parses the regularly updated KGML (KEGG XML)
files into graph models maintaining all essential pathway attributes.
The package offers functionalities including parsing, graph operation,
visualization and etc.
License: GPL (>=2)
LazyLoad: yes
Depends: methods, XML (>= 1.96-0), graph
Suggests: RBGL, Rgraphviz (>= 1.18.0), KEGG.db
Collate: kegg2graph-functions.R parse.R graph.R kgmlfile.R misc.R vis.R
URL: http://www.dkfz.de/en/mga/index.html
biocViews: Pathways

This should show up in the devel branch in the next couple of days.  I
am just a messenger here so if it helps you, be sure to thank the
maintainer.


  Marc





Sim, Fraser wrote:
> Hi Anand-
>
> I searched for a similar package in the archives but I think the KEGG
> database is not available in a format that describes the 'edges' in a
> manner which can be easily parsed into a graph object.
>
> Biocarta on the otherhand does have this information available as an xml
> file.
>
> I have written some code to parse Biocarta and plot pathways accordingly
> using graphviz. I was thinking about making this available as a package
> but haven't gotten around to it yet. 
>
> Cheers,
> Fraser
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Anand Gavai
> Sent: Thursday, December 11, 2008 7:46 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Kegg pathway --> gene network
>
> Hi Everyone,
>
> I had been searching over google but to no avail. Actually I had been
> searching on the net for any equivalent package in bioconductor which
> would
> help the community to construct an equivalent gene network from
> available
> pathway database like KEGG. 
>
> For e.g. To find all genes available in Glycolysis pathway and depending
> on
> the direction of arcs between metabolites, to construct an equivalent
> gene
> regulatory network from the same.
>
>  
>
> off course doing this manually and construct a graphNel object is
> possible,
> but to do this for more pathways would be cumbersome, so was wondering
> if
> there are any tools available in this regard or any pointers  .?
>
>  
>
> Any information would be of great help.
>
>  
>
> Thanks in advance,
>
> Anand
>
>  
>
>
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>
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