[BioC] biomaRt query

Wolfgang Huber huber at ebi.ac.uk
Thu Dec 11 22:24:00 CET 2008

Dear Sebastian

thank you. This is turning not really to be a "biomaRt" (the R package) 
question, but one for "Ensembl" (the online database). I think they'd be 
happy to hear your feedback (including all the other many genes you 

Go to Ensembl http://www.ensembl.org/info/website/help and select 
"contact helpdesk".

I did find "TWIST2" in Ensembl, but apparently the association with the 
EntrezGene ID is not present in all datasets produced by the Biomart 
database warehouse.

Best wishes

Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber

Sebastien Gerega ha scritto:
> I thought that might be the case, I was just surprised by how many genes 
> didn't show up in Ensembl....
> Sean Davis wrote:
>> On Tue, Dec 9, 2008 at 7:21 PM, Sebastien Gerega <seb at gerega.net> wrote:
>>> Hi,
>>> there is probably a very simple answer to this question but why does the
>>> following code produce the output NULL?
>>> ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl")
>>> getBM(attributes = c("entrezgene", "hgnc_symbol"), filters = 
>>> "entrezgene",
>>> values = "117581", mart = ensembl, na.value = NA)
>>> The NCBI site has a hgnc symbol listed for the gene:
>>> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=117581 
>> If you do a similar search at Ensembl, it appears that Ensembl does
>> not have an entry for TWIST2.  (I did the search quickly, so I could
>> be mistaken.)  Remember that these genome databases do not always
>> agree about what a gene represents (or even which ones exist).
>> Sean

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