[ensembl-dev] Bug?? Biomart mapping of Mouse ID to MGI ids

Ragavendran, Ashok ARAGAVENDRAN at mgh.harvard.edu
Fri Sep 4 15:14:52 BST 2015


hi Magali,

   Thanks again for the prompt response. This again relates back to my
previous post on the Entrez IDs and the webpage issue

   
http://useast.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000106677;r=5:87459490-87490871;t=ENSMUST00000147854

   
http://useast.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000029268;r=5:87459490-87482260

As you can see each of the genes above are assigned to only one MGI id
which was misleading whereby I was unsure what the correct  set of
results were.

Does this mean we should not rely on the search results for a gene and
for anything definite use the biomart tool instead??

Please don't get me wrong, I think that the Ensembl database is a really
wonderful resource and I just wanted to bring these aspects to your
attention in the hope that it helps in making it better.

 Furthermore, if I search using ensembl gene id for Ugt2a1 i get the
following results
        Ensembl Gene ID    Associated Gene Name    MGI ID    MGI
symbol    Ensembl Transcript ID
        ENSMUSG00000106677    Ugt2a1    MGI:2149905    Ugt2a1   
ENSMUST00000147854

Whereas results from MGI data show that ENSMUSG00000106677  is 
associated with both MG1 ids.
>From MGI database:

MGI:2149905    Ugt2a1    O    Gene    UDP glucuronosyltransferase 2
family, polypeptide A1    43.56    5    87459490    87490871    -   
BB375653|AK140757|AF184901|BC048926    NM_053184   
OTTMUST00000066277|OTTMUST00000138762   
ENSMUST00000079811|ENSMUST00000144144|ENSMUST00000147854           
OTTMUSP00000033195|OTTMUSP00000072911   
ENSMUSP00000078740|ENSMUSP00000114842|ENSMUSP00000114583    NP_444414

MGI:3576095    Ugt2a2    O    Gene    UDP glucuronosyltransferase 2
family, polypeptide A2    43.56    5    87459493    87482258    -   
BC058786|BC048920    NM_001024148   
OTTMUST00000066277|OTTMUST00000138762   
ENSMUST00000144144|ENSMUST00000147854|ENSMUST00000079811           
OTTMUSP00000072911|OTTMUSP00000033195   
ENSMUSP00000078740|ENSMUSP00000114842|ENSMUSP00000114583    NP_001019319

I see their web page is inconsistent and only lists one of the Ensembl
gene IDs, I will write them and see if they can correct the inconsitency.


Thanks again for all your help.

Cheers
    Ashok

On 9/4/15 7:00 AM, dev-request at ensembl.org wrote:
> Message: 1
> Date: Fri, 04 Sep 2015 10:11:35 +0100
> From: mag <mr6 at ebi.ac.uk>
> Subject: Re: [ensembl-dev] Bug?? Biomart mapping of Mouse ID to MGI
> 	ids
> To: dev at ensembl.org
> Message-ID: <55E96047.5010702 at ebi.ac.uk>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hi Ashok,
>
> MGI mappings, like HGNC mappings, are direct mappings we import directly 
> from the source.
> According to this database, both Ugt2a1 and Ugt2a2 map to the Ensembl gene.
> http://www.informatics.jax.org/marker/MGI:2149905
> http://www.informatics.jax.org/marker/MGI:3576095
>
> Looking at the gene models, there is an overlap with ENSMUSG00000106677, 
> which corresponds to Ugt2a1.
> I suspect MGI:2149905 needs to be updated to link to ENSMUSG00000106677 
> instead of ENSMUSG00000029268, but we cannot change it at our end.
> If you have any experimental evidence to correct those mappings, please 
> contact MGI (mgi-help at jax.org) to let them know.
>
>
> Regards,
> Magali
>
> On 03/09/2015 21:34, Ragavendran, Ashok wrote:
>> > Hello,
>> >      I have come upon a subsequent bug where there is an erroneous
>> > mapping of Ensembl Mouse ID to the corresponding MGI:ID using BioMart (
>> > both in bioconductor and the Ensembl web interface). Please let me know
>> > if I am missing something in this regard. Correct mapping should be only
>> > to 3576095 and not to 2149905.
>> >
>> >      Cheers
>> >      Ashok
>> >
>> > ===== Text based Results from querying the gene id  ENSMUSG00000029268
>> > =======
>> >
>> > Ensembl Gene ID    Status (gene)    MGI ID    MGI symbol
>> > ENSMUSG00000029268    KNOWN    MGI:2149905    Ugt2a1
>> > ENSMUSG00000029268    KNOWN    MGI:3576095    Ugt2a2
>> >
>
>
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> End of Dev Digest, Vol 63, Issue 4
> **********************************
>

-- 
Ashok Ragavendran
Bioinformatics Specialist
Center for Human Genetic Research
Massachusetts General Hospital
Richard B. Simches Research Center
185 Cambridge St, Boston MA 02114
aragavendran at mgh.harvard.edu
ph: +1-617-726-1329



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