[BioC] biomaRt query

Sebastien Gerega seb at gerega.net
Wed Dec 10 03:55:42 CET 2008

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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