Hi, I have a list of about 5000 metabolites and I'm trying to link them to associated pathways. At the moment I've been manually going through the list and searching them individually in KEGG. Is there a way where I can input the 5000 metabolites into KEGG in one search (rather than have to search each metabolite individually) and it bring up a list of pathways?
Thanks in advance for any help/suggestions!
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samgittings •
You could look at programmatically searching for all 500 metabolites. Here are some places to look for ideas:
I haven't tried each of them but it would be a place to start. If you can give an example metabolite and its corresponding pathways as an example, that would be help in suggesting solutions.
Being more specific, you can find a table joining pathway IDs and compound IDS at
you'd first map the metabolites to their corresponding genes , Then mapping gene to pathway is very easy .
If you don't care the version of kegg . you can just use the R packge .
Or you have to download the newest version of mapping files , and write the script by yourself .
These posts might be helpful
Retriving compounds name from KEGG IDs
Genes to KEGG
Gene Set Clustering based on Functional annotation (GeneSCF)
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