Hi Hao, In addition to the method that my colleague provided, you can also get the RefSeq gene symbol from the refGene table (and skip the kgXref table). Select the RefSeq Genes track in the Table Browser as before, and choose to get "selected fields from primary and related tables." Then choose the "name2" field from the refGene table (in addition to any other fields you wish to retrieve). That field should contain the gene symbol that is displayed in the RefSeq Genes track.
If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 4/4/12 3:32 PM, robert kuhn wrote: > Hello, Hao, > > You can use the Table Browser to get this relationship. > > set for hg19: > group: Genes and Gene Predicions > track: refSeq Genes > identifiers: [paste list] > NM_001130986 > output format: selected fields from primary and related tables > [get output] > > check name, chrom, chromStart, chromEnd or whatever you want > > in Linked Tables section: > check kgXref [Allow Selection From check Tables] > > in hg19.kgXref: > check geneSymbol [get output] > > result: > > #hg19.refGene.name hg19.refGene.chrom hg19.refGene.txStart > hg19.refGene.txEnd hg19.kgXref.geneSymbol > NM_001130986 chr2 71693831 71913893 DYSF > > best regards, > > --b0b kuhn > ucsc genome bioinformatics group > > > On 4/4/2012 3:12 PM, Zhao, Hao wrote: >> Hi UCSC Genome Browser friends, >> >> I am writing to ask a very common question about converting refseq id to >> gene symbol. One solution is to look for the mapping in the kgXref table. >> However, there are still quite a number of refSeq IDs lack of gene symbols. >> For example, NM_001130986 is not in the kgXref table. But we find it >> correspond to a gene "DYSF" in the genome browser. I wonder if there is a >> more complete table than kgXref for the refSeq ID to gene symbol mapping. >> >> Thank you very much. >> Hao >> >> MD Anderson >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
