Question: View gene list in GAGE enriched terms
1
gravatar for mbk0asis
18 months ago by
mbk0asis470
Korea, Republic Of
mbk0asis470 wrote:

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 • 463 views
ADD COMMENTlink modified 5 months ago by giderk0 • written 18 months ago by mbk0asis470

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) 

#Search02010, 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)
ADD REPLYlink modified 10 days ago • written 10 days ago by andrea_chi0
0
gravatar for giderk
5 months ago by
giderk0
giderk0 wrote:

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' )
ADD COMMENTlink modified 5 months ago • written 5 months ago by giderk0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 960 users visited in the last hour