Question: How to get a list of genes and interactions from KEGG signaling pathways map?
0
gravatar for zeyu.wang.ustc
3 months ago by
zeyu.wang.ustc0 wrote:

I want to get a list of genes and interactions from the maps.

http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&map=map04630&keyword=stat

However, it looks like the rest api is not working (http://rest.kegg.jp/link/genes/hsa05223 )

Any else ways to do that?

genome • 223 views
ADD COMMENTlink modified 3 months ago by genomax46k • written 3 months ago by zeyu.wang.ustc0
0
gravatar for theobroma22
3 months ago by
theobroma221.1k
theobroma221.1k wrote:

You can download the KGML/XML file for each pathway of interest from KEGG.

ADD COMMENTlink written 3 months ago by theobroma221.1k

how to do that? .........................................

ADD REPLYlink written 3 months ago by zeyu.wang.ustc0

Well, you can do it manually from the KEGG website...it should be in the list to the right of the pathway. Alternatively, you can use the xml package in R if you require all pathways for your taxid of interest. Help is out there!

ADD REPLYlink written 3 months ago by theobroma221.1k
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