Now I'm doing enrichment using clusterprofiler and WebGestalR. In clusterprofiler:

x <- unique(unlist(as.list(org.Bt.egGO2ALLEGS)))
length(x)#5586

there are 5586 genes with GO annotation.

In WebGestalR:

enrichD_BP <- loadGeneSet(organism = "btaurus",enrichDatabase = "geneontology_Biological_Process_noRedundant") geneSet_BP <- enrichD_BP$geneSet length(unique(geneSet_BP$gene))#9011

enrichD_CC <- loadGeneSet(organism = "btaurus",enrichDatabase = "geneontology_Cellular_Component_noRedundant") geneSet_CC <- enrichD_CC$geneSet length(unique(geneSet_CC$gene))#6224

enrichD_MF <- loadGeneSet(organism = "btaurus",enrichDatabase = "geneontology_Molecular_Function_noRedundant") geneSet_MF <- enrichD_MF$geneSet length(unique(geneSet_MF$gene))#7960

geneSet <- unique(c(unique(geneSet_BP$gene),unique(geneSet_CC$gene),unique(geneSet_MF$gene)))
length(geneSet)#10085

There are at least 10085 genes with GO annotation.

WebGestalR has more gene set than clusterprofiler. So which one is the most up to date and same with online GO database? But how to get the gene set from online GO database. This question has puzzled me these days. Becasue I think they two are powerful and should have the same results

WebGestaltR is a CRAN package and is beyond the scope of this support site. In addition, this support site is primarily intended to help people with technical questions about using Bioconductor tools. You are asking a qualitative question about the underlying data source for two unrelated packages, which is really something you should be checking yourself. The data source for the org.Bt.eg.db package is provided by the show method.

> library(AnnotationHub)
> hub <- AnnotationHub()
snapshotDate(): 2022-04-21
> z <- hub[["AH100401"]]
loading from cache
> z
OrgDb object:
| DBSCHEMAVERSION: 2.1
| Db type: OrgDb
| Supporting package: AnnotationDbi
| DBSCHEMA: BOVINE_DB
| ORGANISM: Bos taurus
| SPECIES: Bovine
| EGSOURCEDATE: 2022-Mar17
| EGSOURCENAME: Entrez Gene
| EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| CENTRALID: EG
| TAXID: 9913
| GOSOURCENAME: Gene Ontology
| GOSOURCEURL: http://current.geneontology.org/ontology/go-basic.obo
| GOSOURCEDATE: 2022-03-10
| GOEGSOURCEDATE: 2022-Mar17
| GOEGSOURCENAME: Entrez Gene
| GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| KEGGSOURCENAME: KEGG GENOME
| KEGGSOURCEURL: ftp://ftp.genome.jp/pub/kegg/genomes
| KEGGSOURCEDATE: 2011-Mar15
| GPSOURCENAME: UCSC Genome Bioinformatics (Bos taurus)
| GPSOURCEURL: 
| GPSOURCEDATE: 2021-Mar15
| ENSOURCEDATE: 2021-Dec21
| ENSOURCENAME: Ensembl
| ENSOURCEURL: ftp://ftp.ensembl.org/pub/current_fasta
| UPSOURCENAME: Uniprot
| UPSOURCEURL: http://www.UniProt.org/
| UPSOURCEDATE: Fri Apr  1 15:06:51 2022

Please see: help('select') for usage information

You can see that we downloaded the go-basic.obo file from geneontology.org on 3/10/2022 and parsed it using Entrez Gene IDs as the source ID.

You will have to read whatever documentation is provided by WebGestaltR to see where they get their data and decide for yourself which one you think is 'better'.