Hello Ying, The UCSC Gene IDs are unique for every transcript. A description of the way the gene set was made is available on the details page for UCSC Genes: http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownGene&db=hg18
This announcement about updating the gene set may also be of interest to you: https://lists.soe.ucsc.edu/pipermail/genome-announce/2008-September/000140.html Finally, you might want to use the tables 'knownCanonical' and knownIsoforms'. The knownCanonical table consists of a representative transcript from each cluster of UCSC Genes. The knownIsoforms table identifies the cluster each transcript belongs to. I hope this is helpful. If you have further questions, please feel free to write back to [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 01/07/10 14:41, Ying Wang wrote: > Dear Sir or Madam, > > I am trying to download the annotation of "UCSC genes" of hg18 from "Tables" in your website. I found that "UCSC genes" use unique naming system, for example , "uc001aaa.2 ", but I am wondering this ID is the isoform's ID or gene's ID. To me ,it seems more like an isoform or transcript ID. so when we need to count the gene's number in "UCSC genes", can we just count the record with different ucsc ID format ,or should we convert the ID to gene name? > > Thank you very much! and look forward to your reply > > Best wishes! > > Ying > > 2010-01-08 > > > > Ying Wang > > > ------------------------------------------------------------------------ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
