KEGG pathway database

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yuechao yang

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Jan 6, 2025, 12:17:36 AMJan 6

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Would you please tell me where you got the database of mus KEGG pathway for GSEA? I didn't see the information from the manul. And the results webgestaltR provided didn't seem to support personlized visualization. Do you have any suggestion?

John Elizarraras

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Jan 16, 2025, 12:31:44 PMJan 16

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Hello,

The KEGG database was created by querying the KEGG api using the KEGGREST R package. You can download the KEGG GMT in WebGestalt from the API: https://2024.webgestalt.org/api/geneset?organism=mmusculus&database=pathway_KEGG&fileType=gmt&version=2024. As for the visualization, are you referencing the color highlighting upon clicking the pathway link?

Could you click on the pathway link and share the URL it directs you to?

Best,

John

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