Hello, The CCDS records are not named with RefSeq identifiers. They are composite sequences derived from multiple sources. They are however linked into the UCSC Genes track, which could be used as a link to other sources (gene name, symbol, refseq accession, etc.)
The Table browser would be a good tool for you to explore. You can use it for queries or simply find out schema information (table contents, data examples/format, common keys to join on) in order to build successful mysql queries. How to do this: from main browser web page click on "Tables". Then adjust clade, genome, etc. all the way down to track = CCDS. For the default (primary) table, click on "describe table schema". This is your information page. Schema at the top, linked tables (including which key is the link to join with), and track description on the bottom. To link from CCDS to UCSC Genes, start with the CCDS track's primary table and link through ccdsKgMap. In the second table is the transcript identifier for the UCSC Genes transcripts. Use this to obtain gene name/symbol information from the kgAlias or kgXref tables or refLink (to start with, there are others to select from, explore to see if useful for you). We hope this helps, Jennifer http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jeffrey Rosenfeld" <[email protected]> wrote: > From: "Jeffrey Rosenfeld" <[email protected]> > To: [email protected] > Sent: Friday, August 21, 2009 11:18:04 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] CCDs gene names and descriptions > > Hi, > > I have been looking at your database without success and I was > hoping > you could help me. I am trying to get a list of all of the CCDS gene > IDs along with the gene names and gene descriptions. I thought that > a > merge of ccdsInfo and refSeqSummary would allow be to link up the > mRNA > description with the summary, but the following MySQL query on your > server turned up nothing: > select ccdsInfo.ccds, refSeqSummary.summary from ccdsInfo, > refSeqSummary > where ccdsInfo.mrnaAcc = refSeqSummary.mrnaAcc; > Empty set (1.11 sec) > > indicating that there is a disconnect between the tables. Is there a > proper way to perform this query, or could you just send me a table? > > Thank you for the help, > > Jeff > > > -- > > Jeffrey Rosenfeld Ph. D. > > Research Scientist > Laboratory of Analytic Genomics, Division of Psychiatry Research, > The Zucker Hillside Hospital; > > North Shore - Long Island Jewish Health System; > > Mailing Address: > The Zucker Hillside Hospital > Psychiatry Research > 75-59 263rd Street > Glen Oaks, NY 11004 > > 718-470-8836 (ph) > 718-343-1659 (fax) > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
