KEGG pathway gene list different from the picture
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6.0 years ago
bharata1803 ▴ 530

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 • 1.8k views
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6.0 years ago
Sam ★ 4.1k

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

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Oh, I see. Thank you.

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