Question: How to get the latest KEGG pathway
0
gravatar for Raymond
20 months ago by
Raymond0
Raymond0 wrote:

Hi, 

    I want to draw KEGG pathways with my nodes colored correlated to p-value*log(foldchange).

From :

http://keggscape.readthedocs.io/en/latest/pythonscripting.html

I used "http://rest.kegg.jp/list/pathway/hsa" to get all human kegg pathways, and "http://rest.kegg.jp/get/' + pathwayid + '/kgml" to download the correspond pathway for cytoscape input.

However, when I checked the xml files, it showed that they were created in May 14, 2014 .

Anyone here knows how to get the latest version of KEGG pathways?

Also, my current strategy is to use "KEGGscape" and my own script to color all nodes according to my own p-values. Any other suggestions?

 

regards,

Raymond

kegggraph kegg kegg.db • 397 views
ADD COMMENTlink written 20 months ago by Raymond0
1

This site is for questions about Bioconductor software, but you don't seem to be using any. If you are not using Bioconductor, please send you questions to another forum such as Biostars.

Anyway, what you get from http://rest.kegg.jp is, by definition, the latest KEGG information. KEGG licensing arrangements prevent anyone from downloading and redistributing KEGG information, so what is on rest.kegg.jp is by far the latest. All other sources are years out of date.

ADD REPLYlink modified 20 months ago • written 20 months ago by Gordon Smyth38k

Thanks for the information, Smyth. 

ADD REPLYlink written 20 months ago by Raymond0
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