Hi, Expression data is contained in tracks in the Expression group, and different data sets are available for different organisms/assemblies. If you are using the GRCh37/hg19 assembly, the GNF Atlas 2 track will probably be the most useful to you.
There is not a straightforward way to add another column with a tissue type (or types), but you can at least filter the expression table to only include your genes of interest. After that, you might try using the "output format: selected fields from primary and related tables" option in the Table Browser to get the data in the format you need. Alternatively, you could check the "Send output to Galaxy" box in the Table Browser and use the tools there (at http://main.g2.bx.psu.edu/) to manipulate your data further. To find the GNF Atlas 2 data in the Table Browser (for the GRCh37/hg19 assembly), select: group: Expression track: GNF Atlas2 table: gnfAtlas2 region: genome Hit the "describe table schema" button to see how the data is organized. The expression level for each of 79 tissues is listed in the "expScores" field. (To see which tissue goes with each experiment ID, select "output format: microarray names" and hit "get output".) To filter on a list of genes, you will need to use UCSC Gene IDs. Please write back to the list if you need help getting the UCSC ID from some other ID. Once you have a list, hit the "filter: create" button and select the "knownToGnfAtlas2" table. Hit "Allow filtering using fields in checked tables". In the "hg19.knownToGnfAtlas2 based filters" section, paste the list of uc identifiers in the "name does match" field and hit submit. Back on the main page, choose the "selected fields" output format, and hit "get output". On this page you can choose which fields you want from the primary table, as well as the knownToGnfAtlas2.name field, so that the gene ID is included. I hope this helps get you the data you are looking for. Please also see the Table Browser User's Guide, here: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Please send any additional questions to [email protected], and we might be able to help you further. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/23/10 20:01, per freem wrote: > Hi, > > I am trying to download a table from the "Tables" section of genome > browser. I used the "Genes and Gene Prediction" tracks of UCSC. I'd > like to get an additional field that says what cell types(s) and/or > tissue(s) the gene is expressed in. I'm looking for data in a tabular > format, so I don't want a high resolution format like BED that tells > me the expression value at each base or something like that, I simply > want another column in the table that says what the cell type/tissue > that this gene is expressed in. > How can I do this? > > Thanks much. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
