Hi Hao, I queried the kgXref table and found records for the two examples you mention:
mysql> select kgID, geneSymbol from kgXref where kgID="uc003lob.1"; +------------+------------+ | kgID | geneSymbol | +------------+------------+ | uc003lob.1 | TCERG1 | +------------+------------+ 1 row in set (0.01 sec) mysql> select kgID, geneSymbol from kgXref where kgID="uc003loc.1"; +------------+------------+ | kgID | geneSymbol | +------------+------------+ | uc003loc.1 | TCERG1 | +------------+------------+ 1 row in set (0.00 sec) The Table Browser is another useful tool you can use to retrieve UCSC IDs and their assoicated gene symbols. Please see this previously answered question for more detailed instructions" https://lists.soe.ucsc.edu/pipermail/genome/2011-July/026488.html Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 1/25/2012 7:13 PM, Zhao, Hao wrote: > Hi UCSC team, > > I am using the UCSC known gene (hg18) as annotation. And I use kgXref.txt > to convert UCSC transcript IDs to refSeq IDs and assign them gene symbols > accordingly. However, I found that some genes do not have gene symbols in > kgXref.txt. For instance, the transcript 'uc003lob.1' is an isoform of the > gene 'TCERG1'--the other isoform of this gene is uc003loc.1, which could be > displayed on the genome browser. Neither uc003lob.1 nor uc003loc.1 could > be found in kgXref.txt. > > I wonder if there is a "latest" version of kgXref.txt, or there is a better > file to help convert UCSC IDs to gene symbols. > > Thank you very much. > > Best, > Hao > MD Anderson Cancer Center > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
