R biomaRT and online Biomart(martview) Results do not match

Question

[esaka]

I found ensembl transcript ids for a specific ensembl gene id from R via library(biomaRt) but I got less transcripts than I got via online Biomart.

i.e

mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
results <- getBM(attributes = c("ensembl_gene_id", "ensembl_transcript_id"),
                 filters = "ensembl_gene_id", values = 'ENSG00000000003', mart = mart)

 results
  ensembl_gene_id ensembl_transcript_id
1 ENSG00000000003       ENST00000373020
2 ENSG00000000003       ENST00000496771
3 ENSG00000000003       ENST00000494424

From website(martview) I got:

ENSG00000000003    ENST00000373020
ENSG00000000003    ENST00000496771
ENSG00000000003    ENST00000494424
ENSG00000000003    ENST00000614008
ENSG00000000003    ENST00000612152

Could you please let me know why the results are different than each other and what should I do to get all transcripts.

Answer 1

[Emily]

It looks like biomaRt is accessing an older version of Ensembl. Here in release 76 we have five transcripts, whereas here in release 75 we have three.

Answer 2

[esaka]

Thank you for clarifying this for me.

I could not find which Ensembl version BiomartRt is using. I guess I need to use Perl API provided by Ensembl to get the results from the last version.

I wish standalone BioMart was not only for Linux distributions. I like the idea of creating your own plugins according to your needs but I am not a Linux user.