How can we find the list of genes involved in each pathway using Gage?

Question

[Tania]

Hi all
If we detected the pathways using gage, how can I find the list of genes involved in each pathway? I mean how to output the genes enriched significanlty in each pathway that was in my list of genes?

res$symbol <- mapIds(org.Hs.eg.db,
                         keys=row.names(res),
                         column="SYMBOL",
                         keytype="SYMBOL",
                         multiVals="first")
    res$entrez <- mapIds(org.Hs.eg.db,
                         keys=row.names(res),
                         column="ENTREZID",
                         keytype="SYMBOL",
                         multiVals="first")
    foldchanges = res$logfc
    names(foldchanges) = res$entrez
    #---------------Use Kegg and gage to get upregulated and downregulated pathways
    datakegg.gs)
    keggres = gage(foldchanges, gsets =kegg.gs, same.dir =,True,  compare="unpaired" )

    lapply(keggres, head)
    keggrespathwaysup = data.frame(id=rownames(keggres$greater), keggres$greater) %>%
      tbl_df() %>%
      filter(row_number()<=5) %>%
      .$id %>%
      as.character()
    keggrespathwaysdn = data.frame(id=rownames(keggres$less), keggres$less) %>%
      tbl_df() %>%
      filter(row_number()<=5) %>%
      .$id %>%
      as.character()
    write.csv(keggrespathwaysup, "keggspathsup.csv")
    write.csv(keggrespathwaysdn, "keggspathsdn.csv")
    #-------------------------------------------------------
    keggresidsup = substr(keggrespathwaysup, start=1, stop=8)
    keggresidsup
    keggresidsdn = substr(keggrespathwaysdn, start=1, stop=8)
    gobpres = gage(foldchanges, gsets=kegg.gs, same.dir =TRUE, compare ="unpaired")
    lapply(gobpres, head)
    plot_pathway = function(pid) pathview(gene.data=foldchanges,gene.idtype="ENTREZID", pathway.id=pid, 
    species="hsa", new.signature=FALSE)

    #------------------------------plot multiple pathways ups and downs
     tmpup = sapply(keggresidsup, function(pid) pathview(gene.data=foldchanges,gene.idtype="ENTREZID", pathway.id=pid, species="hsa"))
    tmpdn = sapply(keggresidsdn, function(pid) pathview(gene.data=foldchanges,gene.idtype="ENTREZID", pathway.id=pid, species="hsa"))

Answer 1

[giderk]

It seems like you can use the essGene function that gage provides. If you just want to see all genes in your data set that overlap with a certain pathway, see this post A: View gene list in GAGE enriched terms