Extracting List Of Genes Associated With A Pathway In Kegg

Question

[Dataminer]

Hi!

Is their a way to extract a list of genes present in a KEGG pathway.

For instance if I want to extraxct list of genes associated with Pathways of cancer, how can I do it?

Thank you

[carolminnicelli]

Is it possible to extract a list of genes of a particular pathway without specifying an organism? For exemple, all genes related to methane pathway used in bacteria...

Thank you.

Answer 1

[Damian Kao]

You can use the KEGG web service (http://www.kegg.jp/kegg/docs/keggapi.html). For exampe:

http://rest.kegg.jp/get/hsa05200

That will give you the entire cancer pathway entry.

Using the linked entries service, you can do this:

http://rest.kegg.jp/link/genes/hsa05200

That'll give you all the genes linked to the cancer pathway.

I am not sure how to post to the web service. I don't think you can. So if you want to get the individual gene entries, you'll have to parse the gene names with a script and use the get service like this (10 at a time):

http://rest.kegg.jp/get/hsa:10000+hsa:1017+hsa:1019

I haven't used this myself, but here is also a bioconductor package: KEGGREST

http://www.bioconductor.org/packages/2.12/bioc/html/KEGGREST.html

[naving2uk]

Kindly how can we detect pathways for the list of gene groups using R? I used KEGGREST but, I do not know if its retrieve the pathway for a list of gene ID's from Affymetrix? Please need help.

[daimin0514]

Since the text in http://rest.kegg.jp/link/genes/hsa05200 is regular, so we can just replace "path:hsa04360 hsa: " with empty string "", then we can easily get the list of Entrez GeneID.

path:hsa04360   hsa:10154 
path:hsa04360   hsa:1020 
path:hsa04360   hsa:10298 
path:hsa04360   hsa:10371 
path:hsa04360   hsa:10500 
path:hsa04360   hsa:10501

Answer 2

[Pierre Lindenbaum]

Using TOGOWS and Damian's example:

Get the genes for hsa05200 as JSON

http://togows.dbcls.jp/entry/pathway/hsa05200/genes.json

[
    {
        "1871": "E2F3; E2F transcription factor 3 [KO:K06620]",
        "23604": "DAPK2; death-associated protein kinase 2 [KO:K08803] [EC:2.7.11.1]",
        "10319": "LAMC3; laminin, gamma 3 [KO:K06247]",
       (...)
        "4292": "MLH1; mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli) [KO:K08734]",
        "1870": "E2F2; E2F transcription factor 2 [KO:K09389]",
        "868": "CBLB; Cbl proto-oncogene, E3 ubiquitin protein ligase B [KO:K04707] [EC:6.3.2.19]",
        "5155": "PDGFB; platelet-derived growth factor beta polypeptide [KO:K04359]",
        "1495": "CTNNA1; catenin (cadherin-associated protein), alpha 1, 102kDa [KO:K05691]"
    }

[Abdullah]

I' trying to get all the genes that metabolism related using the same method you suggested. However, I get an empty list.

http://togows.dbcls.jp/entry/pathway/hsa01100/genes.json

can you please tell me what is wrong?

[Dataman]

Nothing is wrong! You are getting an empty list because there is no gene listed under this entry (i.e. hsa01100). You can check it here and here that no genes are listed.