Hello. Based on what you've described, it sounds like you would like to get a listing of genes that is filtered based on gene ontology. You can do this using our Table Brower. If you're unfamiliar with the Table Browser, please see the User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
Perform the following steps: 1. In your browser, go to http://genome.ucsc.edu/cgi-bin/hgTables 2. Set the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Genes and Gene Prediction Tracks Track: UCSC Genes Table: knownGene Region: genome Output format: selected fields from primary and related tables (you can also check the "Galaxy" checkbox on this line to send your output to Galaxy) 3. Next, you will need to create a filter that will list only the results you're looking for. On the "filter" line, click the "create" button. 4. Scroll down to the "Linked Tables" section and check the "go.goaPart" checkbox. 5. Scroll to the bottom of the page and click the "allow filtering using fields in checked tables" button. 6. Scroll down to the "Linked Tables" section and check the "go.term" checkbox. 7. Repeat step 5. 8. In the "go.term based filters" section, enter exactly the following in the "Free-form query" box: name like "%cytoplasm%" 9. Click the "submit" button. 10. Click the "get output" button. 11. Repeat steps 4-7. 12. In the "Select Fields from hg19.knownGene" section, check the checkboxes of the fields you would like to include in your output. 13. In the "go.term fields" section, check the "name" checkbox. 14. Click the "get output" button (or the "done with selections" button if sending to Galaxy). Note that in step 8, the term you enter between the % symbols is whatever term you are trying to filter. If you enter %cytoplasm% as listed in step 8, any record that contains "cytoplasm" anywhere in that field will appear in your output. You can revise your filter term based on your desired output. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of i b Sent: Tuesday, July 17, 2012 2:06 PM To: [email protected]; [email protected] Subject: [Genome] UCSC tools Hi, is there a way to create a job in my galaxy history from UCSC genome browser that contains a specific set of genes encoding for example only for nuclear or cytoplasmatic proteins proteins? How can I do that? Thanks a lot! ngs-ib _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
