When querying for the gene symbol for ensembl ID, I often have unmatch results. That being said, if I search for these IDs on ensembl website (Grch37 build), I can find them. Below is a list of ensembl IDs with the gene symbol, which I could only retrieve via the website.
ENSG00000017373 SRCIN1
ENSG00000090920 FCGBP
ENSG00000108264 TADA2A
ENSG00000108272 DHRS11
ENSG00000108278 ZNHIT3
ENSG00000121848 RNF115
ENSG00000135213 POM121C
ENSG00000154768 C17orf50
ENSG00000160828 STAG3L2
ENSG00000163386 NBPF10
ENSG00000163486 SRGAP2
ENSG00000165388 ZNF488
ENSG00000168274 HIST1H2AE
ENSG00000168614 NBPF9
ENSG00000170866 LILRA3
In biomaRt, I tried...
library(biomaRt)
gene_list = c('ENSG00000017373', 'ENSG00000090920', 'ENSG00000108264', 'ENSG00000108272')
mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
results <- getBM(attributes = c('ensembl_gene_id', 'external_gene_name'),
filters = "ensembl_gene_id",
values = gene_list,
mart = mart)
And in mygene, I tried...
mg = mygene.MyGeneInfo()
ginfo = mg.querymany(gene_list, scopes='ensembl.gene', fields='symbol', species='human')
I have tried messing with mygene scopes and biomaRt's filters. But for whatever reason, I can only obtain this information on ensembl's website.
As I doubt the website would be more comprehensive than the actual databases, I am looking for feedback on where I may be going wrong.