View gene list in GAGE enriched terms
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3.5 years ago
mbk0asis ▴ 630

Hi.

I just ran "GAGE" to identified GO terms enriched in DEGs.

The results showed the terms and statistics, but not the genes included in each term.

Is there a way to obtain the gene list in each term?

Thank you!

gage gsea gene ontology • 1.1k views
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Hi,

I had the same question and now it is solved. There are two ways to do it.

Solution 1 (in RStudio):

> datakegg.sets.mm)

Then check "kegg.sets.mm" in the "environment". You can use "search" on the right up corner to find the target and click the "value". It will show in the console.

Solution 2:

>library(org.Mm.eg.db)
>mapped <- mappedkeys(org.Mm.egPATH2EG)
>L <- as.list(org.Mm.egPATH2EG[mapped])
>Kegg_ID <- names(L)
>Gene_IDs <- sapply(L, paste, collapse=",")
>KEGGlist<-cbind(Kegg_ID, Gene_IDs) 

´╝âSearch02010, method1
> KEGG02010genes <- KEGG_GeneList["02010",] 
> KEGG02010genes< paste(KEGG02010genes)

#Search02010, method2
> KEGG02010genes <- KEGG_GeneList[KEGG_GeneList$Kegg_ID %in% c("02010"), ]
> KEGG02010genes< paste(KEGG02010genes) 

#Search02010, method3
>KEGG02010genes <- as.character(paste(KEGG_GeneList["02010",2]))
>KEGG02010genes

#if table is needed
>write.table(cbind(Kegg_ID, Gene_IDs), file="KEGG to Genes.txt", sep="\t", row.names=FALSE, col.names=FALSE)
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Entering edit mode
2.4 years ago
giderk • 0

GAGE has functions for extracting essential genes, but if you just want to see which of your genes overlap with a pathway of interest, you could do something like this below. In the example, the pathway of interest is in "quotes", and you will need to replace YOUR_GENE_SET, Mus.musculus, and kegg.sets.mm with the objects you are working with.

glist<-unlist( kegg.sets.mm["mmu04622 RIG-I-like receptor signaling pathway"])
aa<-glist[glist %in% names(YOUR_GENE_SET)]
mapIds(Mus.musculus, aa , 'SYMBOL' , 'ENTREZID' )
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