KEGG pathway mapping for metabolites

Question

[samgittings]

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!

Answer 1

[erictleung]

You could look at programmatically searching for all 500 metabolites. Here are some places to look for ideas:

• KEGG API http://www.kegg.jp/kegg/rest/keggapi.html
• KEGG module in Biopython http://biopython.org/DIST/docs/api/Bio.KEGG-module.html
• KEGGREST package in R's Bioconductor http://bioconductor.org/packages/release/bioc/html/KEGGREST.html

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.

[lljotall]

Being more specific, you can find a table joining pathway IDs and compound IDS at

[http://rest.kegg.jp/link/cpd/pathway][1]

Answer 2

[jimmy_zeng]

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 .

Answer 3

[EagleEye]

These posts might be helpful

Retriving compounds name from KEGG IDs

Genes to KEGG

Gene Set Clustering based on Functional annotation (GeneSCF)