[Genome] Matching 'known genes' to geneIDs in NCBI

[Fan Hsu]

Hi Su Yeon,

Not sure what you meant by NCBI geneIDs.  If you meant gene symbols,
please be aware that often one gene symbol may represent multiple
alternative splice isoforms.  If you meant RefSeq IDs, then
you can easily just filter out Known Genes entries with names that are
not like "NM_....", but this approach will loose quite a few
valid gene entries and not all RefSeq genes are included
in UCSC Known Genes set because of questionable gene model.

You may want to consider using the kgXref table (cross-reference table of
Known Gens), which has the following fields:

+-------------+--------------+------+-----+---------+-------+
| Field       | Type         | Null | Key | Default | Extra |
+-------------+--------------+------+-----+---------+-------+
| kgID        | varchar(40)  |      | MUL |         |       |
| mRNA        | varchar(40)  | YES  | MUL | NULL    |       |
| spID        | varchar(40)  | YES  | MUL | NULL    |       |
| spDisplayID | varchar(40)  | YES  | MUL | NULL    |       |
| geneSymbol  | varchar(40)  | YES  | MUL | NULL    |       |
| refseq      | varchar(40)  | YES  | MUL | NULL    |       |
| protAcc     | varchar(40)  | YES  | MUL | NULL    |       |
| description | varchar(255) | YES  |     | NULL    |       |
+-------------+--------------+------+-----+---------+-------+

Fan.
-----Original Message-----
From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On
Behalf Of Su Yeon Kim
Sent: Thursday, January 18, 2007 10:34 AM
To: genome at soe.ucsc.edu
Subject: [Genome] Matching 'known genes' to geneIDs in NCBI



Hello,

I would like to have list of known genes that contains
  the geneIDs that are used in NCBI since it seems
easier to use those geneIDs for searching
recent information about the genes and for GO analysis.

How can I get those lists?

Thank you.

Su Yeon






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