Is there any database or tool to get the list of pathways which a gene(Homo sapiens) is involved? Like, Gene Symbol and list of pathways it is involved.
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written
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Pranavathiyani G
This is simple to do programmatically with the PaxtoolsR R library. PaxtoolsR lets you explore pathway information for about 15+ pathway databases from Pathway Commons.
library(paxtoolsr)
geneSets <- downloadPc2("PathwayCommons.8.All.GSEA.hgnc.gmt.gz")
# You can search for multiple genes at once
idx <- searchListOfVectors(c("CHEK2", "FANCE"), geneSets)
names(geneSets)[idx$FANCE]
# RESULTS: There can be duplicate pathways across different data providers
# [1] "9606: BARD1 signaling events" "9606: Fanconi Anemia Pathway" "9606: Fanconi anemia pathway" "9606: Homo sapiens"
# Same search, but only with Reactome data provider
# NOTE: Run downloadPc2() without parameters to see other GSEA possibilities
geneSets <- downloadPc2("PathwayCommons.8.Reactome.GSEA.hgnc.gmt.gz")
idx <- searchListOfVectors(c("CHEK2", "FANCE"), geneSets)
names(geneSets)[idx$FANCE]
# [1] "9606: DNA Repair" "9606: Fanconi Anemia pathway"
I get an error: Error in strsplit(tmp3, ";") : non-character argument when I run geneSets <- downloadPc2("Pathway Commons.7.All.GSEA.hgnc.gmt.gz")
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