Dears,

It makes no sense for me to have different GO enrichment results just because I changed the the type of Gene IDs. Can someone help me out by explaining the reason behind this problem?

I got different results of GO enrichement analysis with different keyTypes using clusterprofiler.

I used top 50 upregulated genes with ENSEMBL ID to show this preoblem.  The organism I used was non-mode animal sheep (Ovis aries). So I created the OrgDb first. And then I used this OrgDb to do GO enrichment analysis.

library(AnnotationHub)
library(clusterProfiler)
hub<-AnnotationHub()
query(hub, c("ovis","OrgDb")) #org.Ovis_aries.eg.sqlite seems to be our orgDb
ovis<-hub[["AH66408"]] #through accession number to get the data

When I used the ENSEMBL IDs to do the GO enrichment analysis. No enrichment terms showed up.

ens.up <- c("ENSOARG00000001333", "ENSOARG00000018254", "ENSOARG00000008212", "ENSOARG00000013893","ENSOARG00000011331",
           "ENSOARG00000009412", "ENSOARG00000011128", "ENSOARG00000016625", "ENSOARG00000005493", "ENSOARG00000010832",
           "ENSOARG00000002845", "ENSOARG00000019791", "ENSOARG00000018325", "ENSOARG00000011952", "ENSOARG00000012714",
           "ENSOARG00000016983", "ENSOARG00000016920", "ENSOARG00000020162", "ENSOARG00000005835", "ENSOARG00000004205",
           "ENSOARG00000008571", "ENSOARG00000007379", "ENSOARG00000018126", "ENSOARG00000006185", "ENSOARG00000012333",
           "ENSOARG00000016101", "ENSOARG00000006969", "ENSOARG00000010787", "ENSOARG00000006789", "ENSOARG00000006474",
           "ENSOARG00000005124", "ENSOARG00000011841", "ENSOARG00000005226", "ENSOARG00000016371", "ENSOARG00000015788",
           "ENSOARG00000000540", "ENSOARG00000007053", "ENSOARG00000001849", "ENSOARG00000008891", "ENSOARG00000008859",
           "ENSOARG00000014867", "ENSOARG00000004306", "ENSOARG00000019690", "ENSOARG00000007524", "ENSOARG00000013119",
           "ENSOARG00000016353", "ENSOARG00000005981", "ENSOARG00000011280", "ENSOARG00000020521", "ENSOARG00000012641")

ego<-enrichGO(gene = ens.up,
                    OrgDb = ovis,
                    ont = "ALL",
                    keyType = "ENSEMBL",
                    pAdjustMethod = "fdr",
                    pvalueCutoff = 0.05,
                    readable = TRUE)
#no enriched terms
#no results

Then I changed the ENSEMBL ID to ENTREZID (concerns about this: 24% genes failed to map). Then I used the ENTREZID to do the enrichment analysis. Some terms are enriched.

ens.en <- bitr(ens.up, fromType = "ENSEMBL",
                  toType = c("ENTREZID"),
                  OrgDb = ovis)
#but 24% of input gene IDs are fail to map...

ego.en<-enrichGO(gene = ens.en$ENTREZID,
                 OrgDb = ovis,
                 ont = "ALL",
                 keyType = "ENTREZID",
                 pAdjustMethod = "fdr",
                 pvalueCutoff = 0.05,
                 readable = TRUE)
#got enrichment terms
#show the results first 3 terms
summary(ego.en)[1:3,1:6]

 ONTOLOGY         ID                  Description GeneRatio  BgRatio       pvalue
GO:0043604       BP GO:0043604   amide biosynthetic process     10/27 228/4322 5.241532e-07
GO:0006412       BP GO:0006412                  translation      9/27 193/4322 1.366523e-06
GO:0043043       BP GO:0043043 peptide biosynthetic process      9/27 197/4322 1.624584e-06