List Of Genes Involved In Metabolic Pathway

Question

[ChIP]

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

[PoGibas]

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

[Neilfws]

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

[ChIP]

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

[PoGibas]

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

[Neilfws]

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.

Answer 1

[Jelena Aleksic]

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

Answer 2

[Peter Karp]

There are a number of ways to do this via MetaCyc 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.