R biomaRT and online Biomart(martview) Results do not match
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Entering edit mode
7.9 years ago
esaka • 0

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.

ensembl biomart martview • 2.6k views
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3
Entering edit mode
7.9 years ago
Emily 23k

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.

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Entering edit mode
7.9 years ago
esaka • 0

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.

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