Question: 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.

library(clusterProfiler)
library(org.Hs.eg.db)

###mtDNA genes
genes<-c("ENSG00000198886","ENSG00000198888","ENSG00000198763","ENSG00000198840","ENSG00000212907","ENSG00000198786","ENSG00000198695","ENSG00000198727","ENSG00000198804","ENSG00000198712","ENSG00000198938","ENSG00000198899","ENSG00000228253")

ego<-enrichGO(genes, OrgDb = org.Hs.eg.db, 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?

Cheers,

Answer: ```

> genes<-c("ENSG00000198886","ENSG00000198888","ENSG00000198763","ENSG00000198840","ENSG00000212907","ENSG00000198786","ENSG00000198695","ENSG00000198727","ENSG00000198804","ENSG00000198712","ENSG00000198938","ENSG00000198899","ENSG00000228253")
>
>
> ego<-enrichGO(genes, OrgDb = org.Hs.eg.db, 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
qvalue
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
geneID
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
Count
GO:0098800 12
GO:0070469 11
GO:0044455 12
GO:0098798 12
GO:0098803 10
GO:0005746 10
```