[Genome] Error in the Zebrafish genome Ensembl Gene Xref data

[Hiram Clawson]

Good Morning Jun Yin:

Thank you for bringing this table to our attention.  This table,
ensGeneXref and the table ensInfo that you find in the Zebrafish
danRer5/July 2007 genome browser are obsolete tables that referenced
Ensembl version 46.  The correct Ensembl genes currently available
on the genome browser are now Ensembl version 49.  Please discard
the table data you have downloaded.  We will be deleting that
obsolete table from the genome browser.  To see the relationships
of the Ensembl genes to their evidence mRNAs, please follow
the Ensembl gene links from the UCSC genome browser to the
Ensembl genome browser.  All evidence for Ensembl gene predictions
can be found in the Ensembl genome browser.  UCSC no longer attempts
to copy that evidence data to the UCSC genome browser.

--Hiram

Jun Yin wrote:
> Dear Sir or Madam,
> 
> I am a Ph.D. student in University College Dublin. My work subject is mainly on bioinformatics and computational biology.
> 
> About two days ago, I download the Zebrafish genome Ensembl Gene Xref data from UCSC ftp site. Here is the link:
> http://hgdownload.cse.ucsc.edu/goldenPath/danRer5/database/ensGeneXref.txt.gz 
> 
> It seems there are some errors in this file. For example, when I check the link sequence of Ensembl gene "ENSDARG00000002536" in EMBL, it tells the EMBL id is "BC045915". But, in fact, the EMBL id should be "BC055558". And, for example, the EMBL id for "ENSDARG00000071239" in ensGeneXref.txt is "BC055558", but if fact, it should be "BX649337". I think most of the other linkages between EnsGene and EMBL ids are wrong in this file.
> 
> I dont know whether there are any other errors in this file. Please check it and fix it.
> 
> Best regards,
> 
> 
> 
> 
> Jun Yin
> Ph.D. candidate in U.C.D.
> 2008-04-29
> 
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin