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?
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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.
Thanks! Is there any database or flat file I can download which maps VEGA gene names to ENSG IDs?
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
would you please describe the first method in more detail, i.e. where to find this dropdown menu?
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.