[Genome] HUGO gene symbols

[Fan Hsu]

This user's question seems can be answered by some query to public MySQL DB.
kgXref and/or kgAlias would be a good candiate table.

Not sure if current TB can pull it off.  I vaguely remember there
was some discussion on adding the function to enable users to paste
in a list of gene symbols and get result just as if pasting in
a list of accession numbers.  I guess it is on someone's todo list.

Fan.
-----Original Message-----
From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On
Behalf Of Deepak Grover
Sent: Monday, March 19, 2007 1:42 PM
To: genome at soe.ucsc.edu
Subject: [Genome] HUGO gene symbols


Hi there,



I am having some difficulty while searching HUGO gene symbols in UCSC table
browser, will really appreciate if you can help me with these. The problem
is as follows.



I have been trying to retrieve various kinds of information (like gene
summary, homologs etc.) for a set of 100 odd HUGO gene symbols that I have.
The first observation is that these can not be used directly as identifiers,
as  there is no field corresponding to HUGO gene symbols in refseqsummary,
BlastTab and some other tables that I tried to search. I found that HUGO
symbols will correspond to "name2" field in the refgene table, but don't
know of a way to search for identifiers from a table if they are not the
primary field.



Only table, that I found having them as primary field, was hgncXref in
proteome. I tried to search that table by pasting my list of 100 mouse gene
symbols. To my surprise, the result completely ignored the identifiers and
reported all the 22000 mouse genes, rather than the 100 I searched (any idea
why that might be happening?).



I have been facing these difficulties previously also, when I solved this by
writing few PERL scripts. However, I am curious to know whether there exists
a way in Genome Browser to perform this job. I will really appreciate any
clue or tips to approach the problem.



Thanks



Deepak Grover

Postdoctoral Fellow

School of Medicine

Johns Hopkins University

600 N. Wolfe St. / Meyer 4-163

Baltimore, MD 21287

410.502.5740

dgrover6 at jhmi.edu





_______________________________________________
Genome maillist  -  Genome at soe.ucsc.edu
http://www.soe.ucsc.edu/mailman/listinfo/genome