Ensembl ID to Gene Symbol Converter

Question

[GA]

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!

[GenoMax]

This is a frequently asked question with multiple prior threads:

How to use biomart on R to convert Ensembl Gene IDs to Symbols?
Question: Convert Ensembl Transcript Ids Ensmust To Gene Symbol In R
converting mouse emsembl gene IDs to Gene names by bioMart and gconvert with no luck

Answer 1

[ATpoint]

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.

[GA]

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

[GenoMax]

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

[GA]

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

Answer 2

[Ben Moore]

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/