In my first approach to the use of Gene Ontology, I have found a discordance if we consult either Mouse Genome Informatics (MGI) or Ensembl for these data.
However these numbers are different according to Ensembl data retrieved through R/Bioconductor. In particular, for Zic2 (Id 22772) the difference is very significant (24 terms in MGI vs. only 3 terms in Ensembl):
> my_ensembl = useMart ("ensembl", dataset = "mmusculus_gene_ensembl") > getBM (attributes = "go_id", filters ="entrezgene" , values = '22771', mart = my_ensembl) go_id 1 GO:0003676 2 GO:0046872 3 GO:0003677 4 GO:0005634 ../.. 22 GO:0008589 23 GO:0007389 24 GO:0021510 25 GO:0042472 > getBM (attributes = "go_id", filters ="entrezgene" , values = '22772', mart = my_ensembl) go_id 1 GO:0003676 2 GO:0005634 3 GO:0016604 >
So, my questions are: Which is the reason for this discordance? Has it something to do with the different types of evidence to assign GO terms? Also, in order to proceed to analysis like GO enrichment, which of these two databases would be more appropriate?