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

[Ragavendran, Ashok]

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<mailto:dev-request at ensembl.org> wrote:

Message: 1
Date: Fri, 04 Sep 2015 10:11:35 +0100
From: mag <mr6 at ebi.ac.uk><mailto:mr6 at ebi.ac.uk>
Subject: Re: [ensembl-dev] Bug?? Biomart mapping of Mouse ID to MGI
        ids
To: dev at ensembl.org<mailto:dev at ensembl.org>
Message-ID: <55E96047.5010702 at ebi.ac.uk><mailto: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<mailto: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
>







--
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<mailto:aragavendran at mgh.harvard.edu>
ph: +1-617-726-1329


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