Question: List Of Genes Involved In Metabolic Pathway
1
gravatar for ChIP
5.9 years ago by
ChIP490
Netherlands
ChIP490 wrote:

Hi!

I was wondering if their was a way to get a list of genes involved in metabolic pathways (KEGG or any other repository).

Just to be more clear, I am talking about the genes in reference pathway http://www.genome.jp/kegg/pathway/map/map01100.html

Kindly let me, how can I get this list.

thank you

pathway enrichment • 8.3k views
ADD COMMENTlink modified 4.3 years ago by Peter Karp30 • written 5.9 years ago by ChIP490
5

Please see Extracting list of genes associated with a pathway in KEGG

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by PoGibas4.8k
3

Yes, asked, answered and discussed very recently. It's always a good first step to search the site for similar questions before posting.

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by Neilfws48k

Yeah, well that page does not say anything about extracting the genes involved in metabolic pathways (if you can only tell me the hsaXXXXX code to get the genes cited in metabolic pathways I will be more than happy). Just to be more clear I am talking about the genes in reference pathway (Metabolic Pathways). http://www.genome.jp/kegg/pathway/map/map01100.html

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by ChIP490

Select pathway of interest (under the Pathway menu);
Select organism -> Go;
Under the Pathway entry get pathway number (for example for human Purine metabolism you get hsa00230);
See the link in my comment -> Damian post -> He uses hsa05200 in http://rest.kegg.jp/link/genes/hsa05200 -> replace ending with your number -> http://rest.kegg.jp/link/genes/hsa00230 -> Download genes

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by PoGibas4.8k

The reference pathway (1) by definition is not linked to any particular organism and (2) is an overview of all metabolism and hence, pretty much all genes. So what you are asking is not especially sensible.

ADD REPLYlink written 5.9 years ago by Neilfws48k
1
gravatar for Jelena Aleksic
5.9 years ago by
Cambridge, UK
Jelena Aleksic900 wrote:

MetabolicMine has a template that does it: http://metabolicmine.org/beta/template.do?name=PathwayGenes&scope=all

ADD COMMENTlink written 5.9 years ago by Jelena Aleksic900
0
gravatar for Peter Karp
4.3 years ago by
Peter Karp30
United States
Peter Karp30 wrote:

There are a number of ways to do this via MetaCyc (http://metacyc.org/) or other databases in the BioCyc collection, including:

  1. Go to a pathway page and then click the Download Genes command in the right-sidebar menu
  2. If you create a SmartTable containing one or more pathways, and then choose "Genes of pathway" from the Transforms menu above, you will get a table showing all genes present in each of the pathways.

 

ADD COMMENTlink written 4.3 years ago by Peter Karp30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 983 users visited in the last hour