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Question: How to get a list of genes and interactions from KEGG signaling pathways map?
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gravatar for zeyu.wang.ustc
3 months ago by
zeyu.wang.ustc • 0
zeyu.wang.ustc • 0 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 COMMENT • link •
modified 3 months ago by genomax ♦ 46k • written 3 months ago by zeyu.wang.ustc • 0
0
gravatar for theobroma22
3 months ago by
theobroma22 • 1.1k
theobroma22 • 1.1k wrote:

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

ADD COMMENT • link written 3 months ago by theobroma22 • 1.1k

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

ADD REPLY • link written 3 months ago by zeyu.wang.ustc • 0

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 REPLY • link written 3 months ago by theobroma22 • 1.1k
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