Hello, Joanna. I believe the confusion you encountered in following the instructions in the previously-answered mailing list question you referenced stems from the fact that the instructions show the use of Gene IDs in the RefSeq ID format (e.g. NM_025597), however, the hgBlastTab identifiers list must be UCSC Gene IDs. I apologize for that confusion. The "paste list" screen does give examples of the format that the Gene IDs should be in, but if you are ever uncertain about data formats in a table, you can always click the "describe table schema" button which lists all of the fields in a table as well as example data from those fields.
It sounds like you already have a list of mouse RefSeq IDs that need to be converted into mouse UCSC Gene IDs. To do so, perform the following steps: 1. In the Table Browser, set genome/assembly to mouse/mm9 2. Set track/table to UCSC Genes/knownGene 3. On the "identifiers" line, click the "paste list" button and paste in your list of IDs 4. Set "output format" to "selected fields from primary and related tables" 5. Click the "get output" button 6. Scroll down to the "Linked Tables" section and check the checkbox next to mm9.refGene 7. Scroll down to the bottom of the page and click the "Allow Selection From Checked Tables" button 8. In the mm9.knownGene section, make sure the "name" checkbox is checked 9. In the mm9.refGene section, make sure the "name" checkbox is checked 10. Click the "get output" button With your output, you can now follow the instructions in the previously-answered mailing list questions to get the human-equivalent UCSC Gene IDs. Afterward, if you would like to obtain the human-equivalent RefSeq IDs, just follow the above steps I outlined using human/hg19 in step 1 and using your hgBlastTab output in step 3. Note that there is not necessarily a 1-to-1 relationship between RefSeq IDs and UCSC Gene IDs. Concerning the GSEA geneset formats, the Table Browser does not support these formats. The Table Browser output is easy enough to import into external programs such as Excel, but if the Table Browser output needs to be modified in any way, it would need to be done using a custom script. 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 Joanna Balcerek Sent: Monday, March 26, 2012 5:18 PM To: [email protected] Subject: [Genome] converting mouse to human gene id's in mass Hello, I have mouse gene ID's from an affymetrix chip that I'd like to convert to orthologous human gene ID's. There are 50k probes, and I was wondering how I could do this in mass? (Or, perhaps, if such data already exists?) I read some online forums, particularly this one<https://lists.soe.ucsc.edu/pipermail/genome/2007-July/014258.html>, which says to paste a list into Tables, using hgBlastTab. I always receive an error doing this, even though I've been trying the same format as the examples listed in the email (NM_...). I am looking to do a GSEA with my samples, and I need the output to be compatible with the GSEA geneset formats. How can I format the data output from the browser? Thank you very much, Joanna _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
