Question: KEGG pathway gene list different from the picture
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gravatar for bharata1803
3.4 years ago by
bharata1803420
Japan
bharata1803420 wrote:

Hello,

I want to map my up/down regulated gene to a pathway and visualize it.

I check a pathway from KEGG database : http://www.genome.jp/kegg-bin/show_pathway?hsa04310 and after that,

I tried to download the gene list using this link : http://togows.dbcls.jp/entry/pathway/hsa04310/genes.json

I noticed that, there are a lot of difference in the gene list compare to the picture. Many genes in the list is not shown in the picture. Is it always like that? Do you have any suggestion how to map my up/down regulated to a pathway network and then visualize it? Thank you very much for your suggestions.

 

kegg pathway • 1.3k views
ADD COMMENTlink modified 3.4 years ago by Sam2.3k • written 3.4 years ago by bharata1803420
1
gravatar for Sam
3.4 years ago by
Sam2.3k
New York
Sam2.3k wrote:

KEGG tends to pool genes from the same class into the same label. So for example, if you click Wnt on the picture, you will get a list of genes, all belong to the Wnt family e.g. WNT16, WNT4 etc. Therefore you would expect that the downloaded information to be much larger than what you saw on the picture

ADD COMMENTlink written 3.4 years ago by Sam2.3k

Oh, I see. Thank you. 

ADD REPLYlink written 3.4 years ago by bharata1803420
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