Question: KEGG pathway mapping for metabolites
0
gravatar for samgittings
2.8 years ago by
samgittings0 wrote:

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!

kegg • 3.4k views
ADD COMMENTlink modified 2.8 years ago by EagleEye6.2k • written 2.8 years ago by samgittings0
1
gravatar for erictleung
2.8 years ago by
erictleung90
United States
erictleung90 wrote:

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.

ADD COMMENTlink written 2.8 years ago by erictleung90

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

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

ADD REPLYlink written 7 days ago by lljotall0
0
gravatar for jimmy_zeng
2.8 years ago by
jimmy_zeng90
University of Macau
jimmy_zeng90 wrote:

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 .

ADD COMMENTlink written 2.8 years ago by jimmy_zeng90
0
gravatar for EagleEye
2.8 years ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

These posts might be helpful

Retriving compounds name from KEGG IDs

Genes to KEGG

Gene Set Clustering based on Functional annotation (GeneSCF)

ADD COMMENTlink written 2.8 years ago by EagleEye6.2k
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