[Genome] HUGO names of known genes

[Fan Hsu]

Hi Ralph,

The geneSymbol field in the kgXref table mostly is the
gene symbol from RefSeq (if a Known Gene's representative mRNA is a RefSeq),
which I believe is usually the same as HUGO/HGNC gene symbol.
If a UCSC Known Gene is not represented by a RefSeq, we use
some additional logic (e.g. get the gene name from the corresponding
UniProt protein) to assign a gene symbol and if this does not work,
we just assign the mRNA ID as the geneSymbol.

If you want very precise HGNC gene symbols, there is an hgncXref table
in our proteome database, which is constructed based on HUGO/HGNC
data directly.  Each record contains HGNC gene symbol, RefSeq ID,
UniProt accession, entrez ID, and a description, not every field
is always filled in though.

Fan.
-----Original Message-----
From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On
Behalf Of Ralph Haygood
Sent: Wednesday, April 19, 2006 11:46 AM
To: genome at soe.ucsc.edu
Cc: rhaygood at duke.edu
Subject: [Genome] HUGO names of known genes


Using the Table Browser, is there a way to get the HUGO name, if any,
associated with a Santa Cruz known gene?  I realize that at least
sometimes the HUGO name is the content of the kgXref.geneSymbol field
and/or among the contents of the kgAlias.alias field, but is there
somewhere I can look and know that if I see something there, it's the
HUGO name?  Thanks.

Ralph Haygood
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