Could someone please recommend a query for getting the proteins that interact with a single gene from Pathway Commons? I would be glad to use paxtoolsr or a raw SPARQL query. I have browsed the documentation for paxtoolsr, but I am having a hard time determining which sources and properties to use.
For the gene PTGS2, I can get the data I want by surfing to http://www.pathwaycommons.org/about/, entering PTGS2 where it says "enter a gene" and clicking "start exploring." That takes me to http://www.pathwaycommons.org/pcviz/#neighborhood/ptgs2 where I click on download to SIF. That gives me http://www.pathwaycommons.org/pc2//graph?source=PTGS2&kind=neighborhood&format=BINARY_SIF
This example is close to what I have in mind, but it takes a path as input, not a single gene.
genes <- c("AKT1", "IRS1", "MTOR", "IGF1R") t1 <- graphPc(source = genes, kind = "PATHSBETWEEN", format = "BINARY_SIF", verbose = TRUE)
thanks,
Mark