Hi Brent, The Table Browser is a useful tool for retrieving gene symbols associated with Affy probes. Click on "Tables" (located on the top blue navigation bar) and make the following selections:
clade: Mammal genome: Human assembly: hg18 (or hg19) group: Expression track: Affy U133 table: affyU133 region: genome output format: selected fields from primary and related tables output file: enter a filename to save your results to a file, or leave blank to display results in the browser file type returned: plain text Click "get output". On the following page, select 'qName' then under "Linked Tables" select 'hg18|knownToU133...'. Click "Allow Selection From Checked Tables". Scroll down and select 'kgXref' under "Linked Tables", then click "Allow Selection From Checked Tables". Finally, select 'geneSymbol' under "hg18.kgXref fields" and click "get ouput". For more information on how to use the Table Browser, please see: http://genome.ucsc.edu/cgi-bin/hgTables#Help I hope this helps. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 9/6/2011 2:07 PM, Brent Pedersen wrote: > Hi, in order to get the gene symbol associated with an affy (affyU133) > probe for hg18/19, I'm using: > > SELECT A.qName, GROUP_CONCAT(DISTINCT X.geneSymbol ORDER BY > X.geneSymbol SEPARATOR ';;;') FROM > affyU133 A, kgXref X, knownToU133 T WHERE > SUBSTR(A.qName, 7, LENGTH(A.qName) - 7) = T.value AND T.name = X.kgID > GROUP BY A.qName LIMIT 20; > > where the substring is because affyU133.qName is prefixed with > "U133A:" or "U133B:" > > Is that the best way to do this join? > > thanks, > -Brent > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
