converting transcript IDs (Ensembl) to gene symbols in R
1
0
Entering edit mode
23 days ago
ashkan ▴ 160

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?

RNA-seq • 239 views
ADD COMMENT
1
Entering edit mode

ashkan : Please do not delete threads that have received a comment/answer.

ADD REPLY
2
Entering edit mode
23 days ago
bk11 ★ 2.6k

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
ADD COMMENT

Login before adding your answer.

Traffic: 2118 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6