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Kegg Map ID from pathway Name

Hi, I have a list of pathway map for which I have no. of enzymes present in my data. Pathway list with no. of enzymes

I have another list that has name of pathway and gene count. Gene count pathway data

I want to get map ID for each pathway in the 2nd picture. One pathway has multiple map ID which is okay but It is taking time to do it manually for a long list. I would appreciate any help. Thank you.

id kegg pathway
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updated by jv jv • written by Space_Life • Space_Life

1 answer

it sounds like what you are looking for are the KEGG gene sets which will contain a list of all the genes within a given pathway for each pathway of interest. It is strongly recommended that you do this programmatically which will not only be more time efficient but also far more reproducible than doing this by hand but the best approach will depend on your preferred scripting language and your level of comfort with scripting.

There are several R packages that include functions to retrieve up-to-date KEGG pathways gene sets which as best I can tell all use the KEGG REST API service for which a good starting point may be http://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html

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written by jv jv

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