[BioC] annotation - biomaRt - getBM - multiple entrez ID for one ensembl ID
Laure Cougnaud
laure.cougnaud at openanalytics.eu
Fri May 3 16:18:22 CEST 2013
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 at uw.edu>
To: "Laure Cougnaud [guest]" <guest at bioconductor.org>
Cc: bioconductor at r-project.org, "laure cougnaud" <laure.cougnaud at 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.
>
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--
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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