[BioC] Visualise KEGG pathway and highlight genes

Georg Otto georg.otto at tuebingen.mpg.de
Fri Apr 17 11:04:40 CEST 2009

Hi Daniel,

Daniel Brewer <daniel.brewer at icr.ac.uk>

>>From a couple of interesting gene lists I have found KEGG pathways which
> contain genes from both lists.  Does anyone know how to visualise this?
>  I was thinking something along the lines of the KEGG pathway being
> plotted and the genes from the two lists highlighted in different colours.
> I can cope with this not being done in bioconductor but would prefer it
> if the final image was exported as PDF. 

if a non-bioconductor solution is ok for you, you should have a look at
pathvisio or genmapp. These programs are able to visualize expression
data in a pathway context. Some pathways KEGG pathways can directly be
used from wikipathways, others you have to convert yourself.



Hope that helps,


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