[BioC] Kegg pathway --> gene network

[Sim, Fraser]

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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