Hello bioconductor experts:
 
now I am using GOstats package to get enriched pathway:
 
> paramsKEGG <- new("KEGGHyperGParams", geneIds = geneCluster,
           universeGeneIds = geneUniverse, annotation = "org.Hs.eg.db",
           pvalueCutoff = 0.1, testDirection = "over")
>output <- summary(hgKEGG_Over)
 
I can get enriched geneSymbol as below. my question is how to correspond these geneSymbol to the entries (enclosed by square) in KEGG pathway figure?
 
>overlap_EGs <- geneCluster[geneCluster %in% unlist(mget(output$KEGGID[1], revmap(org.Hs.egPATH),ifnotfound=NA))]
>overlap_symbols <- mget(overlap_EGs, org.Hs.egSYMBOL)

thanks
Yu
 


      
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