KEGG pathway mapping for metabolites
3
0
Entering edit mode
5.1 years ago

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 • 6.2k views
ADD COMMENT
2
Entering edit mode
5.0 years ago
erictleung ▴ 100

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 COMMENT
0
Entering edit mode

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

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

ADD REPLY
0
Entering edit mode
5.0 years ago
jimmy_zeng ▴ 90

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 COMMENT
0
Entering edit mode
ADD COMMENT

Login before adding your answer.

Traffic: 1827 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6