Question: ensembl transcript id to gene symbol using biomart
0
gravatar for hxlei613
20 months ago by
hxlei61380
Bangladesh
hxlei61380 wrote:

Hi. I am using biomart to convert ensembl transcript id to gene symbol. However there seems to be something wrong. Because in the output there is an ensembl transcript id which has two symbol. Here are my script.

> ensembl <- useMart(host="dec2013.archive.ensembl.org", biomart = "ENSEMBL_MART_ENSEMBL",dataset = "hsapiens_gene_ensembl")
> result <- getBM(attributes=c("ensembl_transcript_id", "hgnc_symbol"), filters = "ensembl_transcript_id", values = values, mart= ensembl)

The output is :

ensembl_transcript_id   hgnc_symbol

 ENST00000226218         SEBOX

ENST00000226218           VTN

In the script I use Ensembl 74: Dec 2013. Then I try Ensembl 75.The output is the same for Ensembl 75. However when I use the archive Ensembl 74 http://dec2013.archive.ensembl.org/index.html to search this transcript id myself, it only shows symbol VTN.

Thanks for any comments.

ensembl biomart R • 2.9k views
ADD COMMENTlink modified 20 months ago by Emily_Ensembl18k • written 20 months ago by hxlei61380

take a look at the id history on the website

ADD REPLYlink written 20 months ago by YaGalbi1.4k
1
gravatar for Emily_Ensembl
20 months ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

Both have been associated as external references in 74: http://dec2013.archive.ensembl.org/Homo_sapiens/Gene/Matches?db=core;g=ENSG00000109072;r=17:26691290-26700110

Pick the gene name rather than the HGNC symbol as attributes to get the gene name that was actually selected for the gene, rather than all that match.

Better yet, don't use four year old databases, use the up-to-date one which only has one HGNC external reference: http://www.ensembl.org/Homo_sapiens/Gene/Matches?db=core;g=ENSG00000109072;r=17:26691290-26700110

ADD COMMENTlink written 20 months ago by Emily_Ensembl18k
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