How to visualise KEGG pathway?
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3.9 years ago
tianshenbio ▴ 180

I am working on a non-model organism and I have already got the enriched kegg pathway and the associated enzymes. Is there a tool I can use to generate a pathway figure highlighting the enzymes (with ko numbers) associated with the enriched pathway? I know there are tools such as pathview but all of them start the analysis from the gene expression matrix...In my case, the enrichment is done...I just need to visualize it.

kegg enrichment RNA-Seq • 3.8k views
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3.9 years ago
ashish ▴ 680

KEGG color pathway is exactly for this purpose. It will give one pathway map for each of your samples. If you have only 2-3 samples you can show all of them in one pathway map using pathview.

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Thank you for your reply. It does the work!

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3.9 years ago
biofalconch ★ 1.1k

I think the r package Pathway is the one you are looking for :)

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3.8 years ago
bigmawen ▴ 430

The name of the package is Pathview instead of Pathway. The r-forge respository is outdated.
Please check out the latest version at GitHub:
https://github.com/datapplab/pathview
or Bioconductor:
https://bioconductor.org/packages/pathview/

you may try the pathview web server if you prefer the GUI:
https://pathview.uncc.edu/

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