[ensembl-dev] Difficulty with finding genes by HUGO name in ensembl database
Michael Schuster
michaels at ebi.ac.uk
Mon Jan 9 15:05:51 GMT 2012
Dear Harish,
This is an exceptional case, as the BAGE3 gene is reported to be in a
location that has rather low sequence quality. A sequence similarity
search suggests it is the processed transcript labelled
RP11-763B22.9-001 (ENST00000444424) in the following display:
http://www.ensembl.org/Homo_sapiens/Location/View?db=core;h=BLAST_NEW:BLA_S6nFdHaJW!!20111117;r=1:148838249-148898456;contigviewbottom=das_DS_775=normal
By following the link, a Genome Reference Consortium DAS track should
be added, showing issues HG-980 (more than half of the BAGE3 gene does
not align) and HG-515 (assembly gap) suggesting a larger problem in
this region.
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/issue_detail.cgi?id=HG-980
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/issue_detail.cgi?id=HG-515
So the GRC looking after the genome sequence for human, mouse and
eventually zebrafish is aware of the issue and awaiting further
experimental data.
Because the BAGE3 gene could not be placed in its entirety and no
coding sequence has been assigned, the closest match for the RefSeq
BAGE3 mRNA is a BAGE2 transcript model. This can be seen on the
following Transcript-Similarity page where NM_182481.1 (BAGE3) matches
with 98% similarity to BAGE2-001 (ENST00000470054).
http://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000187172;r=21:10996026-11098980;t=ENST00000470054
This is most likely the reason why the search engine associated the
string BAGE3 with this BAGE2 transcript and gene.
Regarding your question about the database schema, the following SQL
query indicates how gene symbols are linked to genes. Please note the
object_xref.ensembl_object_type = 'Gene' constraint and the link
between gene.gene_id = object_xref.ensembl_id. Alternatively,
object_xref.ensembl_id can also link to transcript.transcript_id and
translation.translation_id according to the value in
object_xref.ensembl_object_type. However, gene symbols are associated
with genes.
mysql> select gene.stable_id, xref.display_label, xref.dbprimary_acc,
external_db.db_name from gene, object_xref, xref, external_db where
gene.gene_id = object_xref.ensembl_id and
object_xref.ensembl_object_type = 'Gene' and object_xref.xref_id =
xref.xref_id and xref.external_db_id = external_db.external_db_id and
xref.display_label = 'BAGE2';
+-----------------+---------------+---------------+---------+
| stable_id | display_label | dbprimary_acc | db_name |
+-----------------+---------------+---------------+---------+
| ENSG00000187172 | BAGE2 | 15723 | HGNC |
+-----------------+---------------+---------------+---------+
1 row in set (0.00 sec)
The place to see this on the web page would be here:
http://www.ensembl.org/Homo_sapiens/Gene/Matches?db=core;g=ENSG00000187172;r=21:11020842-11098925;t=ENST00000470054
Hope that helps,
Michael Schuster
On 27 Dec 2011, at 22:46, Harish Mahadevan wrote:
> Hi Ensembl dev team,
>
> I recently downloaded the ensembl database and am having some
> difficulty finding genes by HUGO name. For example, there is a gene
> named "BAGE3" that I couldn't find in the ensembl database;
> however, when I searched the ensembl web site (i.e. http://useast.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Gene;end=2;q=BAGE3)
> , I found that "BAGE3" appears to be the same gene as "BAGE2".
>
> Could you point me at the right direction for retrieving gene
> records from the ensembl database (i.e. gene table in "core" schema)
> by HUGO name?
>
> regards
> Harish
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
--
Michael Schuster, Ph.D.
Ensembl Genome Browser Project
Vertebrate Genomics Team
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD
United Kingdom
http://www.ensembl.org/
More information about the Dev
mailing list