converting transcript IDs (Ensembl) to gene symbols in R
I have a list of transcript IDs (Ensembl) and trying to get the gene symbols for all transcripts. so I might have some gene symbols repeated but that is not a problem. I tried to do in R for example using Biomart but did not manage. do you know how I can do it in R?
1 answer
You can do as following:
library(biomaRt)
# Set up the Ensembl BioMart connection
ensembl <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")
# Example list of Ensembl transcript IDs
transcript_ids <- c("ENST00000489730","ENST00000505370","ENST00000608083")
# Retrieve gene IDs corresponding to the transcript IDs
result <- getBM(
attributes = c("ensembl_transcript_id", "ensembl_gene_id","hgnc_symbol"),
filters = "ensembl_transcript_id",
values = transcript_ids,
mart = ensembl
)
result
ensembl_transcript_id ensembl_gene_id hgnc_symbol
1 ENST00000489730 ENSG00000069812 HES2
2 ENST00000505370 ENSG00000197530 MIB2
3 ENST00000608083 ENSG00000097021 ACOT7
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