Ensembl ID to Gene Symbol Converter
2
0
Entering edit mode
8 days ago
GA • 0

I'm trying to convert ensembl gene IDs to gene symbols. The ensembl gene IDs come from human reference file: Homo_sapiens.GRCh38.dna.primary_assembly.fa. I've tried using the BioMart tool from ensembl and the BioTools Converter (https://www.biotools.fr/human/ensembl_symbol_converter), but both tools still give me a lot of blank gene symbols (they don't convert from gene ID to gene symbol). Does anyone know of another gene ID converter that I can try that would give me the complete list of gene symbols for this human reference file?

Thank you!

ensembl Homo_sapiens BioMart biotools • 325 views
ADD COMMENT
1
Entering edit mode
8 days ago
ATpoint 68k

biomaRt is a gold standard tool for this, covered in the comment of GenoMax . Not all gene IDs have an actual gene name. Please show examples of problematic ones, then one can double check.

ADD COMMENT
0
Entering edit mode

For example, these IDs don't convert using biomart:

ENSG00000284928 ENSG00000284930 ENSG00000284931 ENSG00000284932 ENSG00000284934 ENSG00000284946 ENSG00000284948 ENSG00000284951 ENSG00000284952 ENSG00000284954 ENSG00000284956 ENSG00000284957 ENSG00000284959 ENSG00000284962 ENSG00000284964 ENSG00000284966 ENSG00000284968 ENSG00000284969 ENSG00000284976 ENSG00000284977

ADD REPLY
0
Entering edit mode

Checked a couple.

http://www..ensembl.org/Multi/Search/Results?q=ENSG00000284928;site=ensembl - Novel transcript no official name
http://www.ensembl.org/Multi/Search/Results?q=ENSG00000284930 - uncharacterized so no official gene name

ADD REPLY
0
Entering edit mode

How would you recommend I handle these novel transcripts/uncharacterized ones? How would you do it? Should I use the gene symbols for the ones that convert and leave the ensembl IDs for the novel/uncharacterized ones? That might be a little confusing. Is there any other identifier that I could use for the ones that don't have gene names that would make sense to use?

Thank you

ADD REPLY
1
Entering edit mode
19 hours ago
Ben_Ensembl ★ 2.2k

Just to jump in here, Ensembl used to use clone-based names for genes without an official gene symbol. However, since Ensembl 104 we now use the Ensembl stable IDs. More information in the following blog post: https://www.ensembl.info/2021/03/15/retirement-of-clone-based-gene-names/

ADD COMMENT

Login before adding your answer.

Traffic: 2047 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