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Question: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
0
gravatar for Yi-Fang.Wang
2.1 years ago by
United Kingdom
Yi-Fang.Wang0 wrote:

Hi,

I'm trying to use the getEnrichedGO function in the ChIPpeakAnno package for mm9. However, the up-to-date org.Mm.eg.db is mm10. Is there any way to retrieve to mm9 version of the OrgDb object?

Thank you.

 

 

ADD COMMENTlink modified 24 days ago by jun.yu0 • written 2.1 years ago by Yi-Fang.Wang0
2
gravatar for Ou, Jianhong
2.1 years ago by
Ou, Jianhong1000
United States
Ou, Jianhong1000 wrote:

Hi,

This is a very interesting question.  You can download the org.Mm.eg.db of mm9 version at https://www.bioconductor.org/packages/2.7/data/annotation/html/org.Mmu.eg.db.html. To use the last version of OrgDb will affect the gene number of annotated GO terms and the total number of annotated GO terms. You can have a try to liftover the peaks to mm10 and re-annotate the peaks before enrichment analysis.

I try two ways to do enrichment analysis for one hg19 dataset:

1. annotate the peaks by hg19 and getEnrichedGO

2. liftover to hg38 and getEnrichedGO

And compared the results. I found that it will show a little difference.

Here is the code:

> library(ChIPpeakAnno)
> peaks <- toGRanges(system.file("extdata", "MACS2_peaks.xls", package="ChIPpeakAnno"), format="MACS2")
> library(EnsDb.Hsapiens.v75) 
> library(EnsDb.Hsapiens.v79)  
> hg19 <- annoGR(EnsDb.Hsapiens.v75)  
> hg38 <- annoGR(EnsDb.Hsapiens.v79)  
> library(rtracklayer)  
> ch <- import.chain("hg19ToHg38.over.chain") 
> peaks.hg38 <- liftOver(peaks, ch)  
> peaks.hg19 <- annotatePeakInBatch(peaks, AnnotationData=hg19)  
> peaks.hg38 <- unlist(peaks.hg38)  
> peaks.hg38 <- annotatePeakInBatch(peaks.hg38, AnnotationData=hg38)  
> library(org.Hs.eg.db)   
> over.hg19 <- getEnrichedGO(peaks.hg19, "org.Hs.eg.db", condense=TRUE)  
> over.hg38 <- getEnrichedGO(peaks.hg38, "org.Hs.eg.db", condense=TRUE)  
> dim(over.hg19$bp) 
[1] 210  10  
> dim(over.hg38$bp) 
[1] 199  10  
> setdiff(over.hg38$bp[1:20, 1], over.hg19$bp[1:20, 1]) 
[1] "GO:0001503" "GO:0001657"
> setdiff(over.hg19$bp[1:20, 1], over.hg38$bp[1:20, 1]) 
[1] "GO:0000122" "GO:0002262"
> length(intersect(over.hg19$bp[, 1], over.hg38$bp[, 1])) 
[1] 154
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Ou, Jianhong1000
0
gravatar for Yi-Fang.Wang
2.1 years ago by
United Kingdom
Yi-Fang.Wang0 wrote:

Hi Jianhong,

Thank you very much for your reply and sharing your code. The link is exactly what I need.

I have downloaded the org.Mm.eg.db of mm9 version, however, I would like to point out a minor typo in the link, just in case other users might want to download it as well. The mm9 version should be https://www.bioconductor.org/packages/2.7/data/annotation/html/org.Mm.eg.db.html.

 

 

ADD COMMENTlink written 2.1 years ago by Yi-Fang.Wang0
0
gravatar for jun.yu
24 days ago by
jun.yu0
jun.yu0 wrote:

Yi-Fang,

I think org.db is organism level annotation, with is not connected with any specific genome assembly or annotation.

ADD COMMENTlink written 24 days ago by jun.yu0
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