How can I get the list of genes involved in a particular pathway? Is there any tool or database available? For example: mTOR Signaling Pathway How can I find the list of genes which are involved in the pathway.
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Pranavathiyani G
3 answers
Probably multiple ways to get this information from. One is BioSystems database at NCBI. Assuming you want human mTOR data.
Original pathway link.
Here you can get list of genes in volved in mTOR signaling.
http://www.genome.jp/dbget-bin/www_bget?pathway+hsa04150
or use
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.
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