Hi all-

 

Has anyone worked out the problem of getting appropriate graph objects
for the KEGG pathways? I'd like to overlay gene expression data on
specific hyperG over-represented KEGG pathways.

 

The BioC books use the example of the IMCA but does not illustrate how
to use this process generically on other KEGG pathways. The vignette for
the graph package says that this problem was not solved as of 2006. I
read on the mailing list that the cMAP package may be useful but this is
also over 2 years old and I also read that it was not complete c.f. with
the available data on the web.

 

I found the PID on the Nature web site and downloaded an XML file but I
don't see an easy way of mapping the proteins to ENTREZ IDs or similar
atomic identifiers. Has anyone written any code to parse this?

 

Thanks,

Fraser


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