Question: Genes in a Pathway
2
gravatar for Pranavathiyani G
3.5 years ago by
Pondicherry, India
Pranavathiyani G250 wrote:

How can I get the list of genes involved in a particular pathway? Is there any tool or database available? For eg: mTOR Signaling Pathway How can i find the list of genes which are involved in the pathway.

tool database pathway gene • 1.7k views
ADD COMMENTlink modified 3.5 years ago by cannin250 • written 3.5 years ago by Pranavathiyani G250
1
gravatar for genomax
3.5 years ago by
genomax73k
United States
genomax73k wrote:

Probably multiple ways to get this information from. One is BioSystems database at NCBI. Assuming you want human mTOR data.
Original pathway link.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by genomax73k
0
gravatar for EagleEye
3.5 years ago by
EagleEye6.5k
Sweden
EagleEye6.5k wrote:

Here you can get list of genes in volved in mTOR signaling.

http://www.genome.jp/dbget-bin/www_bget?pathway+hsa04150

or use

http://rest.kegg.jp/link/genes/hsa04150

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by EagleEye6.5k
0
gravatar for cannin
3.5 years ago by
cannin250
United States
cannin250 wrote:

Pathway Commons has a download that gives you all the genes for each pathway in the Pathway Commons database:

http://www.pathwaycommons.org/pc2/downloads http://www.pathwaycommons.org/pc2/downloads/Pathway%20Commons.7.All.GSEA.hgnc.gmt.gz

With the paxtoolsr R package, you can get these as a list of vectors that is easy to iterate over.

ADD COMMENTlink written 3.5 years ago by cannin250
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