[BioC] unable to find known entrezgene with biomaRt

Dick Beyer dbeyer at u.washington.edu
Sat Jan 19 21:20:27 CET 2008


Hi Steffen,

Thanks very much for your help.  I am definitely learning here from you and Jim.

Cheers,
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, Steffen Durinck wrote:

> Hi Dick,
>
> For most of the ids, your mapping from entrezgene to hgnc_symbol should work well in Ensembl and correspond to the Entrezgene annotation.  However as Jim mentioned these are two independent groups and e.g. Ensembl updates every two months so if something changed in Entrezgene in those two months you'll need to wait until the next Ensembl release for this to be visible.  Checking EntrezGene for  3514 gives on the upper right hand side "updated 06-Jan-2008"  So this entry was updated (or maybe even just added) after the last Ensembl release (December 2007) which probably explains why it's not in Ensembl yet.
>
> Cheers,
> Steffen
>
> ----- Original Message -----
> From: Dick Beyer <dbeyer at u.washington.edu>
> Date: Saturday, January 19, 2008 8:13 am
> Subject: Re: [BioC] unable to find known entrezgene with biomaRt
> To: "James W. MacDonald" <jmacdon at med.umich.edu>
> Cc: Bioconductor <bioconductor at stat.math.ethz.ch>
>
>> 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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>>>
>>
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