Biomart mapping ensembl_transcript_id_version

Question

[christoph.neu]

Hello,
i have a list of ensembl_transcript_id_version, and I want to map the ensembl_gene_id and external_gene_name to it. However, it does not find a hit for a lot of genes (e.g. the id: ENSMUST00000109424.2, only if I change the version from .2 to .3).

ensembl <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", 
                        host = "www.ensembl.org")
mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL",
                         dataset = "mmusculus_gene_ensembl", 
                         host="www.ensembl.org")

transcript2gene_test1 <- biomaRt::getBM(attributes = 
        c("ensembl_transcript_id_version", "ensembl_gene_id", "external_gene_name"),
        filters=c('ensembl_transcript_id_version'),
        values = c("ENSMUST00000109424.2","ENSMUST00000109424.3") ,
        mart = mart)

Is it possible to find a match for transcripts like ENSMUST00000109424.2, or do I have to remove the version number and just query for ENSMUST00000109424 (Or does this has other downsides.)

Thanks in advance.

[Ram]

I think it would be fine to query for just the transcript_id and exclude the version in your case. Odds are, gene name and gene ID won't change between transcript versions.

Answer 1

[Ben_Ensembl]

Hi Christoph,

I agree with RamRS that querying for the stable ID without the version number will be fine for many cases. However, you could also consider using the ID History Convertor tool to get the up-to-date versioned stable ID: http://www.ensembl.org/Homo_sapiens/Tools/IDMapper

Best wishes

Ben
Ensembl Helpdesk

[christoph.neu]

Thanks, then I will just use the no-Version approach. (Also, because I am not sure whether I use the tool you mention correctly. If I query for ENSMUST00000109424.2 , I get no results.)

[Ben_Ensembl]

If you enter the unversioned stable ID into the ID History Convertor, it will provide you with the timeline of the version increases and the current version number.

[christoph.neu]

thanks, this way it works.