[Genome] Canonical and Non-Canonical table

[Kayla Smith]

Hello Siddarth,

Here is a previously answered mailinglist question similar to yours:
https://www.soe.ucsc.edu/pipermail/genome/2005-July/008123.html

I hope this answers your question.

Kayla Smith
UCSC Genome Bioinformatics Group

SiddarthGautham Selvaraj wrote:
> Hi
> 
> I am siddarth, graduate student in Arizona State University. I got the
> following query.
> 
> Many HGNC genes have records in the Knowngene table but not in
> KnownCanonical table. I have attached a file that contains gene symbols that
> do not have an entry in KnownCanonical but has lot of entries in the
> Knowngene table.
> 
> How to arise conclusions from it? How does UCSC define genes as canonical
> and non canonical. (i.e) When does a gene gains entry in to a
> KnownCanonical table from Knowngene table?
> 
> Thanks
> siddarth
> 
> On 09/01/2008, SiddarthGautham Selvaraj <sselvar1 at asu.edu> wrote:
>> Ya I only mistook them as junk. Pardon me.
>>
>> Thanks
>> siddarth
>>
>> On 09/01/2008, Brooke Rhead < rhead at soe.ucsc.edu > wrote:
>>> Hello again Siddarth,
>>>
>>> A colleague has pointed out that the names like MARCH1 and C10orf10 are
>>> indeed approved gene symbols in HUGO/HGNC.
>>>
>>> If you look them up at http://www.genenames.org/ you will see entries
>>> for them:
>>>
>>> MARCH1 = membrane-associated ring finger (C3HC4) 1
>>> C10orf10 = chromosome 10 open reading frame 10
>>>
>>> --
>>> Brooke Rhead
>>> UCSC Genome Bioinformatics Group
>>>
>>>
>>> Brooke Rhead wrote:
>>>> Hi Siddarth,
>>>>
>>>> Pardon me, I did not see the names like 'C10orf10' in my original
>>> search
>>>> of kgXref.  I see them now.
>>>>
>>>> When there is a HGNC (HUGO) Gene Symbol available, it will appear in
>>>> this field of this table: kgXref.geneSymbol.  Not all genes in the
>>>> knownGene table have a HGNC Gene Symbol assigned.
>>>>
>>>> There is another table in the 'proteome' database that contains HUGO
>>>> gene symbols and HGNC IDs: 'hgncXref'.
>>>>
>>>> One of our team members has developed a MySQL database query that will
>>>> retrieve the HGNC gene symbols mapped to the knownGene transcript
>>> name:
>>>> SELECT geneSymbol,transcript
>>>> FROM knownCanonical,kgXref,proteome.hgncXref
>>>> WHERE kgXref.kgID=knownCanonical.transcript
>>>> AND kgXref.geneSymbol = proteome.hgncXref.symbol
>>>>
>>>> Also, here are some previously answered questions that pertain to
>>>> getting HUGO gene names from our tables:
>>>>
>>>> http://www.soe.ucsc.edu/pipermail/genome/2006-April/010350.html
>>>> https://www.soe.ucsc.edu/pipermail/genome/2006-September/011570.html
>>>>
>>>> I hope this information is helpful.