Hi Laure,

You might want to ask the Ensembl people directly why they choose these
mappings and send your email to helpdesk@ensembl.org

Cheers,
Steffen


On Fri, May 3, 2013 at 7:18 AM, Laure Cougnaud <
laure.cougnaud@openanalytics.eu> wrote:

> Hi James,
>
> Thanks for your response. Indeed this doesn't seem to be an issue of the
> getBM function, but more about the mapping between the ensembl id and the
> entrez ids.
>
> In my case, I have data from an exon array, so after using RMA with this
> cdf file 'huex10stv2hsensg', I have one value per ENSG, the summarized
> value of all probes targeting this region.
>
> I understand that several entrez ids seem to map within the location of
> ENSG00000215417 (Chromosome 13: 92,000,074-92,006,833), but in my case I
> would be interesting only of the gene ID corresponding to MIR17HG (407975),
> because it is the only ID that mapped totally to the gene location of
> ENSG00000215417.
>
> Also, I was a bit confused by the fact that getBM return several gene IDs,
> but only one symbol (which seems to be the right one for the ENSG), whereas
> the entrez IDs correspond to different gene symbols, as you pointed it out.
>
> Best,
>
> Laure
>
>
> ----- Original Message -----
> From: "James W. MacDonald" <jmacdon@uw.edu>
> To: "Laure Cougnaud [guest]" <guest@bioconductor.org>
> Cc: bioconductor@r-project.org, "laure cougnaud" <
> laure.cougnaud@openanalytics.eu>
> Sent: Friday, May 3, 2013 3:43:19 PM
> Subject: Re: [BioC] annotation - biomaRt - getBM - multiple entrez ID for
> one ensembl ID
>
> Hi Laure,
>
> On 5/3/2013 2:43 AM, Laure Cougnaud [guest] wrote:
> > Hello,
> >
> > I am currently analyzing data from an exon array. After pre-processing
> with RMA, with which I obtain a eSet with ensembl IDs, I would like to
> annotate the gene with Entrez ID. I am using getBM function with as input
> the ensembl gene ID and as output  the entrez gene ID. Here is a part of
> the code I am using :
> > mart<- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> > gene2genomeEx<- getBM(values = ex, filters = "ensembl_gene_id", mart =
> mart, attributes = c("ensembl_gene_id", "entrezgene","hgnc_symbol",
> "external_gene_id", "external_gene_db", "description", "chromosome_name",
> "strand"))
> > However for several genes (and a lot of histone genes), I obtain several
> entrez IDs for the same ensembl ID for example for :
> > ex<- c("ENSG00000215417", "ENSG00000224078", "ENSG00000198366",
> "ENSG00000196176", "ENSG00000166012", "ENSG00000158406",
> "ENSG00000196787"), I obtain :
> >     ensembl_gene_id entrezgene hgnc_symbol external_gene_id
> external_gene_db
> > 1  ENSG00000158406       8294    HIST1H4H         HIST1H4H      HGNC
> Symbol
> > 2  ENSG00000158406       8359    HIST1H4H         HIST1H4H      HGNC
> Symbol
> > 3  ENSG00000158406       8360    HIST1H4H         HIST1H4H      HGNC
> Symbol
> > 4  ENSG00000158406       8361    HIST1H4H         HIST1H4H      HGNC
> Symbol
> > 5  ENSG00000158406       8362    HIST1H4H         HIST1H4H      HGNC
> Symbol
> > 6  ENSG00000158406       8363    HIST1H4H         HIST1H4H      HGNC
> Symbol
> > 7  ENSG00000158406       8364    HIST1H4H         HIST1H4H      HGNC
> Symbol
> > 8  ENSG00000158406       8365    HIST1H4H         HIST1H4H      HGNC
> Symbol
> > 9  ENSG00000158406       8366    HIST1H4H         HIST1H4H      HGNC
> Symbol
> > 10 ENSG00000158406       8367    HIST1H4H         HIST1H4H      HGNC
> Symbol
> > 11 ENSG00000158406       8368    HIST1H4H         HIST1H4H      HGNC
> Symbol
> > 12 ENSG00000158406       8370    HIST1H4H         HIST1H4H      HGNC
> Symbol
> > 13 ENSG00000158406     121504    HIST1H4H         HIST1H4H      HGNC
> Symbol
> > 14 ENSG00000158406     554313    HIST1H4H         HIST1H4H      HGNC
> Symbol
> > 15 ENSG00000166012      79101       TAF1D            TAF1D      HGNC
> Symbol
> > 16 ENSG00000166012     654320       TAF1D            TAF1D      HGNC
> Symbol
> > 17 ENSG00000166012     677792       TAF1D            TAF1D      HGNC
> Symbol
> > 18 ENSG00000166012     677805       TAF1D            TAF1D      HGNC
> Symbol
> > 19 ENSG00000166012     677822       TAF1D            TAF1D      HGNC
> Symbol
> > 20 ENSG00000166012     692063       TAF1D            TAF1D      HGNC
> Symbol
> > 21 ENSG00000166012     692072       TAF1D            TAF1D      HGNC
> Symbol
> > 22 ENSG00000166012  100302240       TAF1D            TAF1D      HGNC
> Symbol
> > 23 ENSG00000196176       8294    HIST1H4A         HIST1H4A      HGNC
> Symbol
> > 24 ENSG00000196176       8359    HIST1H4A         HIST1H4A      HGNC
> Symbol
> > 25 ENSG00000196176       8360    HIST1H4A         HIST1H4A      HGNC
> Symbol
> > 26 ENSG00000196176       8361    HIST1H4A         HIST1H4A      HGNC
> Symbol
> > 27 ENSG00000196176       8362    HIST1H4A         HIST1H4A      HGNC
> Symbol
> > 28 ENSG00000196176       8363    HIST1H4A         HIST1H4A      HGNC
> Symbol
> > 29 ENSG00000196176       8364    HIST1H4A         HIST1H4A      HGNC
> Symbol
> > 30 ENSG00000196176       8365    HIST1H4A         HIST1H4A      HGNC
> Symbol
> > 31 ENSG00000196176       8366    HIST1H4A         HIST1H4A      HGNC
> Symbol
> > 32 ENSG00000196176       8367    HIST1H4A         HIST1H4A      HGNC
> Symbol
> > 33 ENSG00000196176       8368    HIST1H4A         HIST1H4A      HGNC
> Symbol
> > 34 ENSG00000196176       8370    HIST1H4A         HIST1H4A      HGNC
> Symbol
> > 35 ENSG00000196176     121504    HIST1H4A         HIST1H4A      HGNC
> Symbol
> > 36 ENSG00000196176     554313    HIST1H4A         HIST1H4A      HGNC
> Symbol
> > 37 ENSG00000196787       8329   HIST1H2AG        HIST1H2AG      HGNC
> Symbol
> > 38 ENSG00000196787       8330   HIST1H2AG        HIST1H2AG      HGNC
> Symbol
> > 39 ENSG00000196787       8332   HIST1H2AG        HIST1H2AG      HGNC
> Symbol
> > 40 ENSG00000196787       8336   HIST1H2AG        HIST1H2AG      HGNC
> Symbol
> > 41 ENSG00000196787       8969   HIST1H2AG        HIST1H2AG      HGNC
> Symbol
> > 42 ENSG00000196787      85235   HIST1H2AG        HIST1H2AG      HGNC
> Symbol
> > 43 ENSG00000198366       8350    HIST1H3A         HIST1H3A      HGNC
> Symbol
> > 44 ENSG00000198366       8351    HIST1H3A         HIST1H3A      HGNC
> Symbol
> > 45 ENSG00000198366       8352    HIST1H3A         HIST1H3A      HGNC
> Symbol
> > 46 ENSG00000198366       8353    HIST1H3A         HIST1H3A      HGNC
> Symbol
> > 47 ENSG00000198366       8354    HIST1H3A         HIST1H3A      HGNC
> Symbol
> > 48 ENSG00000198366       8355    HIST1H3A         HIST1H3A      HGNC
> Symbol
> > 49 ENSG00000198366       8356    HIST1H3A         HIST1H3A      HGNC
> Symbol
> > 50 ENSG00000198366       8357    HIST1H3A         HIST1H3A      HGNC
> Symbol
> > 51 ENSG00000198366       8358    HIST1H3A         HIST1H3A      HGNC
> Symbol
> > 52 ENSG00000198366       8968    HIST1H3A         HIST1H3A      HGNC
> Symbol
> > 53 ENSG00000215417     406952     MIR17HG          MIR17HG      HGNC
> Symbol
> > 54 ENSG00000215417     406953     MIR17HG          MIR17HG      HGNC
> Symbol
> > 55 ENSG00000215417     406979     MIR17HG          MIR17HG      HGNC
> Symbol
> > 56 ENSG00000215417     406980     MIR17HG          MIR17HG      HGNC
> Symbol
> > 57 ENSG00000215417     406982     MIR17HG          MIR17HG      HGNC
> Symbol
> > 58 ENSG00000215417     407048     MIR17HG          MIR17HG      HGNC
> Symbol
> > 59 ENSG00000215417     407975     MIR17HG          MIR17HG      HGNC
> Symbol
> > 60 ENSG00000224078      91380      SNHG14           SNHG14      HGNC
> Symbol
> > 61 ENSG00000224078  100033444      SNHG14           SNHG14      HGNC
> Symbol
> > 62 ENSG00000224078  100033450      SNHG14           SNHG14      HGNC
> Symbol
> > 63 ENSG00000224078  100033802      SNHG14           SNHG14      HGNC
> Symbol
> > 64 ENSG00000224078  100033820      SNHG14           SNHG14      HGNC
> Symbol
> > 65 ENSG00000224078  100506948      SNHG14           SNHG14      HGNC
> Symbol
> > The description, chromosome_name and strand are the same for each
> ensembl gene ID.
> > I checked manually for the entrez ID which corresponds to the ensembl ID
> in ensembl.org, and I found only one entrezID for each gene. Does anyone
> knows where this problem come from? Is it linked to the nature of my
> request?
>
> I'm not sure where you are looking, but as an example, for
> ENSG00000215417, I see 7 EntrezGene genes on the Ensembl site, just like
> you have here:
>
>
> http://www.ensembl.org/Homo_sapiens/Gene/Matches?g=ENSG00000215417;r=13:92000074-92006833
>
> In addition:
>
>  > mget(get(ex[1], revmap(org.Hs.egENSEMBL)), org.Hs.egSYMBOL)
> $`407975`
> [1] "MIR17HG"
>
> $`406952`
> [1] "MIR17"
>
> $`406953`
> [1] "MIR18A"
>
> $`406979`
> [1] "MIR19A"
>
> $`406980`
> [1] "MIR19B1"
>
> $`406982`
> [1] "MIR20A"
>
> $`407048`
> [1] "MIR92A1"
>
> So I don't see anything unexpected here.
>
> Best,
>
> Jim
> >
> > Thanks in advance for your help,
> >
> > Yours sincerely,
> >
> > Laure Cougnaud
> >
> >
> >   -- output of sessionInfo():
> >
> > R version 2.15.1 (2012-06-22)
> > Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> > locale:
> >   [1] 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
> >   [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=C                 LC_NAME=C
>                LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] biomaRt_2.12.0     affy_1.34.0        Biobase_2.16.0
> BiocGenerics_0.2.0 rj_1.1.0-4
> >
> > loaded via a namespace (and not attached):
> > [1] affyio_1.24.0         BiocInstaller_1.4.7   preprocessCore_1.18.0
> RCurl_1.91-1          rj.gd_1.1.0-1         tools_2.15.1
> > [7] XML_3.9-4             zlibbioc_1.2.0
> >
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
> _______________________________________________
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>

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