Finding all pathways for a gene.

Question

[Pranavathiyani G]

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.

Answer 1

[GenoMax]

http://www.genecards.org/

Answer 2

[cannin]

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"

[discipulus]

I get an error: Error in strsplit(tmp3, ";") : non-character argument when I run geneSets <- downloadPc2("Pathway Commons.7.All.GSEA.hgnc.gmt.gz")

[cannin]

You'll need to update the PaxtoolsR package; there was recent reorganization of data that is caused the issue. Check this issue in the code repository for more information.

[GenoMax]

@cannin: Consider correcting the example above to reflect the changes so the solution is current/valid.

[cannin]

I have now updated the example