How to create a .SIF file?

Question

[jolespin]

I'm trying to create a .SIF file for a gene set. I saw How to create a SIF file to use in Cytoscape? but couldn't find the validate option. I went to save but the XML file wasn't what I was looking for. I'm open to using other resources than string-db but I'd prefer to use either string-db, KEGG, or BioCYC

Answer 1

[cannin]

Here is a potential solution using Pathway Commons and the paxtoolsr R package.

library(paxtoolsr)

# Download complete SIF file
pcSif <- downloadPc2("Pathway Commons.7.HumanCyc.BINARY_SIF.hgnc.sif.gz")

# Genes of interest
tmp <- c("TP53", "AKT1")

# Find SIF rows that contain the genes of interest
idxA <- which(pcSif$PARTICIPANT_A %in% tmp)
idxB <- which(pcSif$PARTICIPANT_B %in% tmp)

# Concatenate row indicies
idxAll <- c(idxA, idxB)

# Show the first few results
# NOTE: Only show the first 3 columns that contain the SIF
head(pcSif[idxAll, 1:3])