[BioC] Visualise KEGG pathway and highlight genes

Saroj K Mohapatra smohapat at vbi.vt.edu
Thu Apr 16 17:13:08 CEST 2009

Hi Daniel:

This is also something in which I am interested, but have not found an easy way yet. 

If KEGG allows the network images to be downloaded in SVG format (currently I found only GIF), then I think there is a way of manually modifying the color of the nodes.

Within the KEGGSOAP package, there is a function called "mark.pathway.by.objects" 

Client-side interface to obtain an url for a KEGG pathway diagram with a given set of genes marked
    Given a KEGG pathway id and a set of KEGG gene ids, the functions return the URL of a KEGG
    pathway diagram with the elements corresponding to the genes marked by red or specified color

I used the example code given there in:
url <- mark.pathway.by.objects("path:eco00260",
                c("eco:b0002", "eco:c00263"))
url <- color.pathway.by.objects("path:eco00260",
                c("eco:b0002", "eco:c00263"),
                c("#ff0000", "#00ff00"), c("#ffff00"
And it creates an image at http://soap.genome.jp/tmp/mark_pathway_www2_api14063/eco00260.gif with the nodes marked.

Best wishes,


----- Original Message -----
From: "Daniel Brewer" <daniel.brewer at icr.ac.uk>
To: "Bioconductor mailing list" <bioconductor at stat.math.ethz.ch>
Sent: Thursday, April 16, 2009 6:50:44 AM GMT -05:00 US/Canada Eastern
Subject: [BioC] Visualise KEGG pathway and highlight genes


>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.  I have searched around without
much luck ... it seems possible that KEGGgraph maybe able to do it but
it is not clear from vignette.


Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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