Hi Anton, Yes, you can use the table browser (with the refSeq > kgXref table) to get the gene symbols for both lists and compare. Though, Galaxy makes this a bit more automated (http://main.g2.bx.psu.edu/).
Go to Galaxy and click Get Data > UCSC Main <http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=http%3A//main.g2.bx.psu.edu/tool_runner&tool_id=ucsc_table_direct1&hgta_compressType=none&sendToGalaxy=1&hgta_outputType=bed> table browser (upper left). Select the genome, assembly, etc, for rat and use refSeq with the kgXref Table. It will show you UCSC's table browser in the process, and paste your list of gene identifiers in. The "send output to Galaxy" box should be checked by default. When you click output it will allow you to send the output to Galaxy. Then do the same for mouse. Once both data sets are there, you can use Galaxy's "Join, Subtract and Group" tool to compare the data sets ("Compare Two Data sets" tool). Just join them on the geneSymbol column. Your output should then be a list of genes they have in common. Let me know if you have any additional questions. - Greg Roe UCSC Genome Bioinformatics Group On 3/7/11 2:25 AM, Anton Kratz wrote: > Dear UCSC team, > > I have a list of some RefSeq-genes in mouse, and a list of some RefSeq-genes > in rat. > > I want to find out which genes are present in both lists. But I can not just > compare the identifiers, as the genes have different IDs in the two species. > > For example, Grid2 (glutamate receptor, ionotropic, delta 2) in rat would > have the identifier NM_024379 and be located at chr4:92642427-94054757, > while in mouse it would be NM_008167 at chr6:63206851-64616273. Still > NM_024379 in rat is the "same" as NM_008167 in mouse. > > What is the best approach to find the same genes in two different lists of > mouse and rat as described? Is it possible to get a list of equivalent > RefSeq identifiers in mouse and rat throught he table browser? > > Thanks, > Anton > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
