Question: Downloadable database for human pathways and the associated genes
0
gravatar for newDNASeqer
4.9 years ago by
newDNASeqer630
United States
newDNASeqer630 wrote:

I've been looking to download human signaling pathways & gene set database. I see that pantherdb.org offers such dataset for download, and I am able to extract signaling pathways and their associated genes, and save them in my local database. However, I noticed that the gene symbols may not the same as Hugo, and have no entrez id. 

I also checked pathway commons website and they do offer a lot of public databases for download, but I found they made the extraction more complicated, because most of the downloadable files are in biopax or other xml formats. I am wondering where I can find a flat text file that has human pathways and genes. 

thanks

database pathway • 1.8k views
ADD COMMENTlink modified 4.9 years ago by Christian2.8k • written 4.9 years ago by newDNASeqer630
3
gravatar for Christian
4.9 years ago by
Christian2.8k
Cambridge, US
Christian2.8k wrote:

PathwayCommons provides their database content also in a format compatible with GSEA analysis, which is a textual format that is easy to parse:

http://www.pathwaycommons.org/pc2/downloads/Pathway%20Commons.4.All.GSEA.gmt.gz

 

ADD COMMENTlink written 4.9 years ago by Christian2.8k
2
gravatar for raunakms
4.9 years ago by
raunakms1.0k
Vancouver, BC, Canada
raunakms1.0k wrote:

You could use MSigDB maintained by the Broad Institute. It has comprehensive collection of genesets as well as Signalling pathways. Additionally you could get the genes in HUGO nomenclature or other other ids. It is free but you just need to create an account on it to access the data. Alternatively KEGG and REACTOME also provide the their respective pathway data. Both are included in MiSigDB too.

ADD COMMENTlink written 4.9 years ago by raunakms1.0k
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