Hi Jessilyn, The data that you were referred to is in a track called HAIB Methyl27. From the main browser page, scroll down to the Regulation group and click on HAIB Mehthyl27 to go to the track controls and description. From here you can read about the track and select what subtracks you'd like to see.
You can use our table browser to determine which of your 600 genes have CpG Islands. To get to the table browser click on "Tables" on the blue bar on the top of the main page. Select the clade, genome, and assembly in which you are interested and make the following selections: group: Genes and Gene Prediction Tracks track: (choose your preferred genes track) table: the default table will be the primary table for that track and is the table you should start with; click "describe table schema" to view descriptions of the table columns. region: genome identifiers: (either paste or upload your list; be sure your format matches the necessary fields described) output format: BED - browser extensible data Click "get output". For more information about using the Table Browser see "Using the Table Browser" by scrolling down past the Table Browser form. It provides brief descriptions of the Table Browser controls. You can also see the "User's Guide" at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Jessilyn Dunn wrote, On 12/22/2010 12:47 PM: > Hello, > I am a first year graduate student, and I am having difficulty addressing a > problem in my lab that I was hoping I could use the genome browser to > answer. I have a list of ~600 genes and I would like to do a methylation > array study to see which genes get methylated under certain conditions. > However, I want to narrow down this list by choosing only those genes that > have the ability to be methylated (I do not know if every gene can be > methylated, and I was hoping to choose just those genes with CpG islands). > > I received a recommendation to use methyl-seq and Infinium 27K array data on > the hg18 freeze on UCSC browser but I cannot seem to find these options in > the browser. Could you point me in the right direction? Also, I was > wondering if there is a less tedious method than typing in the 600 genes one > by one to search for CpG islands. Any insight would be very much > appreciated. Thank you for your help! > Jessilyn > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
