Question: mm9 version for ChIPpeakAnno getEnrichedGO function
gravatar for Yi-Fang.Wang
3.0 years ago by
United Kingdom
Yi-Fang.Wang0 wrote:


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

Thank you.



ADD COMMENTlink modified 12 months ago by jun.yu0 • written 3.0 years ago by Yi-Fang.Wang0
gravatar for Ou, Jianhong
3.0 years ago by
Ou, Jianhong1.1k
United States
Ou, Jianhong1.1k wrote:


This is a very interesting question.  You can download the of mm9 version at 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(   
> over.hg19 <- getEnrichedGO(peaks.hg19, "", condense=TRUE)  
> over.hg38 <- getEnrichedGO(peaks.hg38, "", 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 3.0 years ago • written 3.0 years ago by Ou, Jianhong1.1k
gravatar for Yi-Fang.Wang
3.0 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 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



ADD COMMENTlink written 3.0 years ago by Yi-Fang.Wang0
gravatar for jun.yu
12 months ago by
jun.yu0 wrote:


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

ADD COMMENTlink written 12 months ago by jun.yu0
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