I'm looking for an easy way to retrieve all the genes in a list that are associated with a certain GO term, preferably using R/Bioconductor packages. I'm not interested in under/overrepresentation or enrichment.
For instance, I want a list of all genes known to be located in 'presynaptic endosome' (GO:009883).
ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") #retrieve human.ensembl data via biomaRt go_1 = c("GO:0098830", "GO:0098954", "GO:0099007", "GO:0099067", "GO:0099037", "GO:0098955", "GO:0099592", "GO:0099532") #GO IDs of all terms associated with "presynaptic endosome" (inclusive of child terms) pre.gene.data <- getBM(attributes=c('hgnc_symbol', 'ensembl_gene_id', 'go_id', 'go_linkage_type'), filters = 'go', values = list(go_1), mart = ensembl)
but my code doesn't filter the genes based on the GO terms. It gives me the following output:
GO:0006886 AP3D1 ENSG00000065000 intracellular protein transport IEA GO:0016192 AP3D1 ENSG00000065000 vesicle-mediated transport IEA GO:0030117 AP3D1 ENSG00000065000 membrane coat IEA ... and 49 other entries for the gene "AP3D1"
I'm unable to understand what might be the problem. I replaced the filter "go_id" to "go" because of the updated filters used:listFilters(ensembl).