[Genome] Canonical and Non-Canonical table

[SiddarthGautham Selvaraj]

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.
> > >
> >
>
>
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