Question: bioMart ENSEMBL_MART_VEGA exists?
0
gravatar for michael.j.apostolides
5 months ago by
michael.j.apostolides10 wrote:

I am trying to get "ENSEMBL_MART_VEGA" names for my genes.

For example, the following gene seems to be a havanna/vega annotation: RP4-669L17.2

http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000236601;r=1:453633-460480

When I query the hgnc_symbol from bioMart as follows, I get no corresponding symbol, which is expected:

library("biomaRt")

ensembl <- useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")

conversion <- getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id","hgnc_symbol"), filters = c("ensembl_transcript_id"), values = unique(bed$transcript_id), mart = ensembl)

On the following page, there is this "ENSEMBL_MART_VEGA".

https://m.ensembl.org/info/data/biomart/biomart_r_package.html

However, when I use the listMarts(), I do not get the "ENSEMBL_MART_VEGA" as they do in the above link.

Does anyone know why this might be, or how I might get "vega" gene names for my genes?

biomart vega gene name • 299 views
ADD COMMENTlink written 5 months ago by michael.j.apostolides10

VEGA project has been retired/archived as of February 2017.

Here is the page for the gene you are interested in at that archived site. See the links there to go to the corresponding GRCh38 gene.

ADD REPLYlink modified 5 months ago • written 5 months ago by GenoMax96k

Thanks! Is there any database or flat file I can download which maps VEGA gene names to ENSG IDs?

ADD REPLYlink written 5 months ago by michael.j.apostolides10

You could consider using Ensembl Biomart from the Ensembl 88 archive for GRCh38 mappings (chose 'Vega' from the 'Choose Database dropdown menu'): http://mar2017.archive.ensembl.org/index.html

and the Ensembl 75 archive for GRCh37 mappings: http://feb2014.archive.ensembl.org/index.html

If you would like genome-wide mappings you can download MySQL dumps of the data from the Ensembl FTP site from the appropriate archive: http://ftp.ensembl.org/pub/

or use the public MySQL server: https://www.ensembl.org/info/data/mysql.html

ADD REPLYlink written 5 months ago by Ben_Ensembl1.6k

would you please describe the first method in more detail, i.e. where to find this dropdown menu?

ADD REPLYlink written 9 weeks ago by mousaedrees0

Hi mousaedrees,

You can use the BioMart tool within the Ensembl 88 archive: http://mar2017.archive.ensembl.org/biomart/martview/

You can select Vega 68 from the drop down menu that appears within the BioMart interface.

ADD REPLYlink written 8 weeks ago by Ben_Ensembl1.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2230 users visited in the last hour
_