[BioC] unable to find known entrezgene with biomaRt

[Dick Beyer]

Hi Jim,

Thanks for explaining this to me.  I had assumed that if the gene was in ensembl, then I could get other bits of info such as Entrez Gene ID and such.

Is there some bioconductor way, similar to biomaRt, to access this Entrez Gene ID?  What I am really using the getBM call for is just to get a gene symbol and a gene description given the Entrez Gene ID.

Thanks very much,
Dick  
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer
*******************************************************************************

On Sat, 19 Jan 2008, James W. MacDonald wrote:

> Hi Dick,
>
> I'm not sure I understand your question. When I go to the webpage you 
> reference, there is AFAICT no mention of this gene being the same as Entrez 
> Gene 3514 (other than having the same symbol). Nor does Entrez Gene mention 
> that it is the same as Ensembl Gene ENSG00000211592.
>
> A quick look at the location of the gene would imply that it probably is the 
> same, and not two genes that have the same symbol (which is not unique).
>
> Since both the web interface and the programmatic interface agree, this isn't a 
> matter of inconsistencies between the interfaces, so perhaps the question is 
> why do Entrez Gene and Ensembl not reference each other?
>
> If so, this I think is simply due to the fact that you have two different 
> groups that are doing the annotation, and they are not always perfect at 
> referencing each other.
>
> Best,
>
> Jim
>
>
>
> Dick Beyer wrote:
>> Hello,
>> 
>> I am unable to find some Entrez Gene IDs in the ensembl homo sapiens 
>> database via biomaRt, even though I can access them via the ensembl web.
>> 
>> library(biomaRt)
>> mart <- useMart( "ensembl", dataset="hsapiens_gene_ensembl")
>> 
>> getBM(attributes=c("entrezgene","hgnc_symbol","ensembl_gene_id"),filters="entrezgene",values=3845, 
>> mart=mart)
>>    entrezgene hgnc_symbol ensembl_gene_id
>> 1       3845        KRAS ENSG00000133703
>> 
>> getBM(attributes=c("entrezgene","hgnc_symbol","ensembl_gene_id"),filters="entrezgene",values=3514, 
>> mart=mart)
>> NULL
>> 
>> The ensembl web interface:
>> 
>> http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000211592
>> 
>> shows Entrez Gene ID 3514 corresponds to ensembl_gene_id ENSG00000211592, 
>> IGKC.
>> 
>> I'm curious why my biomaRt session will return good results for some valid 
>> Entrez Gene IDs but not for others.  I'm not sure what to try next.  I'd 
>> very much appreciate any help.
>> 
>> sessionInfo()
>> R version 2.6.1 (2007-11-26)
>> x86_64-redhat-linux-gnu
>> 
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>> 
>> attached base packages:
>> [1] tools     stats     graphics  grDevices utils     datasets  methods
>> [8] base
>> 
>> other attached packages:
>>   [1] topGO_1.4.0         SparseM_0.75        AnnotationDbi_1.0.6
>>   [4] RSQLite_0.6-4       DBI_0.2-4           GO_2.0.1
>>   [7] Biobase_1.16.2      graph_1.16.1        biomaRt_1.12.2
>> [10] RCurl_0.8-3
>> 
>> loaded via a namespace (and not attached):
>> [1] cluster_1.11.9  rcompgen_0.1-17 XML_1.93-2
>> 
>> Thanks much,
>> Dick
>> *******************************************************************************
>> Richard P. Beyer, Ph.D.	University of Washington
>> Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
>> Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
>>  			Seattle, WA 98105-6099
>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
>> http://staff.washington.edu/~dbeyer
>> 
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>