Hi Adam, Thank you for searching the FAQ first! The additional step you would need to take to get the gene symbols for genes in the "UCSC Genes" set would be to choose the output format "selected fields from primary and related tables" and select the "geneSymbol" field from the "kgXref" table.
However, since you are interested in finding a method that will work for a wide range of organisms, I suggest using a different gene set altogether, as UCSC Genes is only available for the human, mouse, and rat assemblies. The RefSeq Genes set is available on every browser, and it is not drastically different from UCSC Genes. (UCSC Genes is based in part on RefSeq Genes. From the hg19 UCSC Genes description page: "Compared to RefSeq, this gene set has generally about 10% more protein-coding genes, approximately five times as many putative non-coding genes, and about twice as many splice variants.") To include the gene symbol for RefSeq Genes, choose the "refGene" table, and be sure to include the "name2" field in your output. There are a few browsers (rat rn4, for instance) where the tables are formatted slightly differently, with no "name2" field. In these instances, you can still get the gene symbol by choosing "selected output from primary and related tables", then choosing the "refFlat" table from the linked tables list, and finally choosing to include the "geneName" field from refFlat. -- Brooke Rhead UCSC Genome Bioinformatics Group On 10/25/10 02:43, Adam Wasserstrom wrote: > Hi, > I am interested in obtaining a list of genes for a set of organisms (human, > mouse, etc.). > I read in the FAQ (http://genome.ucsc.edu/FAQ/FAQdownloads.html) the section > titled 'Obtaining a list of known genes' and went according to the > instructions (although I didn't find the 'Known Genes' track, and rather > chose 'UCSC Genes'; in the table I chose 'knownGene' as written). I received > the table including the name of each gene (e.g. uc002icq.2). I am > specifically interested in the symbol of genes (e.g. BRCA1), which are not > part of this table. How can I obtain a list of all genes including the > symbol? For example, a good data page me is such as: > http://genome.ucsc.edu/cgi-bin/hgGene?db=hg18&hgg_gene=uc002icq.1&hgg_chrom=chr17&hgg_start=38449839&hgg_end=38530994. > If I could obtain a list of links of these pages for all genes that would be > great (please not that I would like to have a general procedure applicable > to a wide range of organisms). Previously there were links at the following > address: http://genome.ucsc.edu/knownGeneList/hg18/top.html, but they do not > seem to be present any more. > Your help is much appreciated, > Best wishes, > Adam > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
