Question: ClusterProfiler fails to find GO terms
gravatar for grant.hovhannisyan
3 months ago by
grant.hovhannisyan1.6k wrote:

Hi all,

I need to assign GO terms to DE genes in R. ClusterProfiler seems to be a popular package for that. But for some reason it either fails to detect GO terms or its GO terms do not coincide with other tools.


###mtDNA genes

ego<-enrichGO(genes, OrgDb =, keytype ="ENSEMBL",ont = "CC",pAdjustMethod = "fdr",pvalueCutoff  = 0.1,  qvalueCutoff  = 0.5)

dotplot(ego, showCategory=30)

The same genes with Panther as expected show mtDNA related GO terms. Other genes from my dataset get enrichments, so apparently the problem is not in gene IDs. What am I doing wrong?


clusterprofiler go rna-seq • 211 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by grant.hovhannisyan1.6k
gravatar for Guangchuang Yu
3 months ago by
Guangchuang Yu2.2k
China/Guangzhou/Southern Medical University
Guangchuang Yu2.2k wrote:

> genes<-c("ENSG00000198886","ENSG00000198888","ENSG00000198763","ENSG00000198840","ENSG00000212907","ENSG00000198786","ENSG00000198695","ENSG00000198727","ENSG00000198804","ENSG00000198712","ENSG00000198938","ENSG00000198899","ENSG00000228253")
> ego<-enrichGO(genes, OrgDb =, keyType ="ENSEMBL",ont = "CC",pAdjustMethod = "fdr",pvalueCutoff  = 0.1,  qvalueCutoff  = 0.5)
> head(ego)
                   ID                                  Description GeneRatio   BgRatio       pvalue     p.adjust
GO:0098800 GO:0098800 inner mitochondrial membrane protein complex     12/13 164/21794 2.828287e-25 8.767691e-24
GO:0070469 GO:0070469                            respiratory chain     11/13 119/21794 6.189305e-24 9.593423e-23
GO:0044455 GO:0044455                  mitochondrial membrane part     12/13 258/21794 7.538998e-23 7.790298e-22
GO:0098798 GO:0098798                mitochondrial protein complex     12/13 302/21794 5.173544e-22 4.009497e-21
GO:0098803 GO:0098803                    respiratory chain complex     10/13 104/21794 1.109666e-21 6.879930e-21
GO:0005746 GO:0005746              mitochondrial respiratory chain     10/13 108/21794 1.645447e-21 8.501478e-21
GO:0098800 1.786287e-24
GO:0070469 1.954517e-23
GO:0044455 1.587157e-22
GO:0098798 8.168754e-22
GO:0098803 1.401683e-21
GO:0005746 1.732050e-21
GO:0098800 ENSG00000198886/ENSG00000198888/ENSG00000198763/ENSG00000198840/ENSG00000212907/ENSG00000198786/ENSG00000198727/ENSG00000198804/ENSG00000198712/ENSG00000198938/ENSG00000198899/ENSG00000228253
GO:0070469                 ENSG00000198886/ENSG00000198888/ENSG00000198763/ENSG00000198840/ENSG00000212907/ENSG00000198786/ENSG00000198695/ENSG00000198727/ENSG00000198804/ENSG00000198712/ENSG00000198938
GO:0044455 ENSG00000198886/ENSG00000198888/ENSG00000198763/ENSG00000198840/ENSG00000212907/ENSG00000198786/ENSG00000198727/ENSG00000198804/ENSG00000198712/ENSG00000198938/ENSG00000198899/ENSG00000228253
GO:0098798 ENSG00000198886/ENSG00000198888/ENSG00000198763/ENSG00000198840/ENSG00000212907/ENSG00000198786/ENSG00000198727/ENSG00000198804/ENSG00000198712/ENSG00000198938/ENSG00000198899/ENSG00000228253
GO:0098803                                 ENSG00000198886/ENSG00000198888/ENSG00000198763/ENSG00000198840/ENSG00000212907/ENSG00000198786/ENSG00000198727/ENSG00000198804/ENSG00000198712/ENSG00000198938
GO:0005746                                 ENSG00000198886/ENSG00000198888/ENSG00000198763/ENSG00000198840/ENSG00000212907/ENSG00000198786/ENSG00000198727/ENSG00000198804/ENSG00000198712/ENSG00000198938
GO:0098800    12
GO:0070469    11
GO:0044455    12
GO:0098798    12
GO:0098803    10
GO:0005746    10
ADD COMMENTlink written 3 months ago by Guangchuang Yu2.2k

Thanks! I am using R v. 3.4.4 and thus clusterProfiler v 3.4.4. So I guess the problem is coming from there. How can I fix the issue in my current version of the package? Or its better to update R?

ADD REPLYlink written 3 months ago by grant.hovhannisyan1.6k
gravatar for grant.hovhannisyan
3 months ago by
grant.hovhannisyan1.6k wrote:

With the hint from @Guangchuang in the post above, I resolved the problem by updating clusteProfiler to the latest version.

For that I had to update R to v. 3.5 for my Ubuntu 16.04

Then install the latest bioconductor version

And resolve the igragh fortrat4 dependancy issue

Hope this will save several hours for people with the same problem

ADD COMMENTlink modified 3 months ago • written 3 months ago by grant.hovhannisyan1.6k
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