Why do I have missing values returned from getBM when converting Ensembl transcript IDs to gene names?

Question

When I run the following R code to convert Ensembl transcript IDs to gene names and Ensembl gene IDs:

mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
ensemble2gene <- getBM(attributes=c("ensembl_transcript_id", 
                                    "external_gene_name",
                                    "ensembl_gene_id"),
                       filters = "ensembl_transcript_id",
                       values = as.list(transcripts), 
                       mart = mart)

some of rows returned have NA values for both the gene name and Ensembl gene ID. This is a bit odd because for example, one of the transcript IDs with missing gene IDs is ENST00000414213 but when I google it, I find that it corresponds to gene ENSG00000235143 (according to this). Why am I getting missing results in getBM then? Is it because maybe the transcript is from an old version of the database? If so, is that the only reason or are there other reasons this could be happening?

Answer 1

Hi An Ignorant Wanderer,

Yes, you're right - ENST00000414213 is a deprecated ID from Ensembl release 75.

https://www.ensembl.org/Homo_sapiens/Transcript/Idhistory?t=ENST00000414213

To convert a list of IDs from GRCh37, you will need to use the GRCh37 dataset. You can do this using the following documentation/example: https://www.ensembl.org/info/data/biomart/biomart_r_package.html