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

If anyone else is wondering, this is extremely straighforward.  I had tried this appraoch several days ago, but got corrupted results in my primary enviroment.  See below if interested.

library(paxtoolsr)
# can visualize with igraph or other libraries
library(igraph)

my.gene <- "PTGS2"
pc.result <-
  graphPc(
    source = my.gene, kind = "NEIGHBORHOOD", format = "BINARY_SIF", verbose = TRUE
  )
my.gene.flag <- pc.result$PARTICIPANT_B == my.gene
ceo.flag <- pc.result$INTERACTION_TYPE == "controls-expression-of"
ceo.frame <- pc.result[ceo.flag & my.gene.flag ,]
# lazy and sloppy elimintation of microRNAs
ceo.frame <- ceo.frame[-grep("^MI", ceo.frame$PARTICIPANT_A) ,]
g <-
  graph.edgelist(as.matrix(ceo.frame[, c(1, 3)]), directed = FALSE)
plot(g, layout = layout.fruchterman.reingold)

Under R 3.2.2, RStudio 0.99.485 on Windows 7, the graphPc query returned 39075 neighbors (as strings) and the script ran to completion.  Under  R 3.2.2, RStudio Server 0.99.485 on CentOS 6.7, I got only 58 neighbors as factors, the warnings below, and nothing after I applied my filters.

Warning messages:
1: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  EOF within quoted string
2: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  number of items read is not a multiple of the number of columns