Extract/include transcript list from GAGE analysis result
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14 months ago

Hi everyone, I'm using GAGE following Deseq2 analysis on my RNAseq data. This means, the analysis is being done on log2FC. I can't see any list of transcripts related to GO terms/pathways that are being enriched. Something like the usual tools of enrichment analysis. Is there any way, I can include genes and extract them in my results?

This is the code I'm using: wt_res is name of my Deseq2 result.

Get the log2fold changes

wt_res.fc <- wt_res$log2FoldChange
names(wt_res.fc) <- wt_res$entrez

Run enrichment analysis on all log2fc

fc.kegg.sigmet.p <- gage(wt_res.fc, gsets = kegg.sigmet.gs)
fc.kegg.sigmet.p.up <- as.data.frame(fc.kegg.sigmet.p$greater)
fc.kegg.sigmet.p.down <- as.data.frame(fc.kegg.sigmet.p$less)

save results

write.csv(fc.kegg.sigmet.p.up, 
          file="NAME.csv")

Partially solved: I now can extract the list of genes in each term by following code: Extract gene list of each term

glist<-unlist(kegg.sigmet.gs["hsa04514 Cell adhesion molecules"])
aa<-glist[glist %in% names(wt_res.fc)]
extrac <- mapIds(org.Hs.eg.db, aa , 'SYMBOL' , 'ENTREZID' )

write.csv(as.data.frame(extrac), 
          file="hsa04514.csv")

But, I still can't get the genes from my dataset that mapped to this term and made it significantly enriched.

RNAseq GAGE • 348 views
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