[BioC] extracting interactions between members of the KEGG pathways

[lilong@isb-sib.ch]

Another issue is availability of cMAP data: data for download is very
different from that driving cMAP online querries.  The downloadable
data is only a small subset of online data, and there are quite
some discrepencies between the two.  The downloadable data is unchanged
since early 2005.

Li

> There is some stuff done in the cMAP and pathRender packages, but this
> has not progressed that far, mostly due to a lack of resources
>
> cMAP is a meta-data package which has information from both KEGG and
> BioCarta (original data from the NCI)
>
> pathRender is in the development archive
>
> best wishes
>    Robert
>
>
> Jane Fridlyand wrote:
>> Hello,
>>
>> I was wondering whether there is an infrastructure in one of the BioC
>> packages to extract connections between members of the KEGG pathways. As
>> far as I can tell KEGG package allows to get the identifiers of the
>> members very easily, however I do not see a way of going one step
>> further
>> so to be able to produce a graph (where presence of each edge indicates
>> known interaction or same compound )
>>
>> Thank you. Any help /suggestion is greatly appreciated.
>>
>> Jane
>>
>>
>>
>>
>>
>> ********************************************************************************
>> Jane Fridlyand, Assistant Professor
>> Department of Epidemiology and Biostatistics
>> Center for Bioinformatics and Molecular Biostatistics
>> UCSF Comprehensive Cancer Center,
>> Box 0128 San Francisco, CA 94143-0128
>> Office: Room N224 Tel: (415)476-0168 Fax: (415)502-3179
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>
> --
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-7700
> rgentlem at fhcrc.org
>
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