[BioC] Kegg pathway --> gene network

Sim, Fraser Fraser_Sim at URMC.Rochester.edu
Thu Dec 11 15:42:09 CET 2008

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

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. 


-----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
help the community to construct an equivalent gene network from
pathway database like KEGG. 

For e.g. To find all genes available in Glycolysis pathway and depending
the direction of arcs between metabolites, to construct an equivalent
regulatory network from the same.


off course doing this manually and construct a graphNel object is
but to do this for more pathways would be cumbersome, so was wondering
there are any tools available in this regard or any pointers  .?


Any information would be of great help.


Thanks in advance,



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