Hello, Karmella. To expand upon Luvina's instructions, to create the filter, perform the following steps in the Table Browser:
1. Select the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Genes and Gene Prediction Tracks Track: UCSC Genes Table: knownCanonical 2. Next to "filter", click the "create" button 3. In the "Linked Tables" section, scroll down and check the hg19.knownGene checkbox 4. Scroll to the bottom of the page and click the "Allow Filtering Using Fields in Checked Tables" button 5. In the "hg19.knownGene based filters" section, the third line should read "strand does match +" 6. Click the "submit" button Also note that these tables: wgEncodeUwHistoneHepg2H3k27me3StdPkRep1 wgEncodeUwHistoneHepg2H3k27me3StdPkRep2 wgEncodeUwHistoneBjH3k27me3StdPkRep1 wgEncodeUwHistoneBjH3k27me3StdPkRep2 contain the methylation scores for H3k27me3 in Hepg and Bj cell lines as calculated according to the process outlined in the UW Histone track description here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeUwHistone and in the reference contained therein. You may also be interested in these additional tables: wgEncodeUwHistoneHepg2H3k27me3StdHotspotsRep1 wgEncodeUwHistoneHepg2H3k27me3StdHotspotsRep2 wgEncodeUwHistoneBjH3k27me3StdHotspotsRep1 wgEncodeUwHistoneBjH3k27me3StdHotspotsRep2 which also contain methylation hotspot data. You can read more about both sets of tables in the aforementioned description. Please be aware that the encode tables contain all the methylation scores, not just the high scores. If you're only interested in the high methylation scores, you'll need to filter the encode tables similar to my above example: 1. Select the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Regulation Track: UW Histone Table: select the appropriate tables 2. Next to "filter", click the "create" button 3. Edit the "score" line so that it contains the values you are interested in such as "score is >= 500" 4. Click the "submit" button I hope this helps. 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 Karmella Haynes Sent: Wednesday, January 25, 2012 12:54 PM To: [email protected] Cc: Carly Hom Subject: [Genome] Genome Browser Question: overlapping histone modification peaks with promoters Good afternoon Luvina, I am a research mentor who is helping an undergrad with her project. Thank you very much for your generous assistance. We have a question about your earlier instructions for finding promoter regions that overlap with histone methylation peaks (H3K27me3). ~~~ "To find the actual transcription start positions, you will need to query the knownCanonical table in the Table Browser (to get only one isoform). You will also need to filter by strand on the knownGene table by clicking on the 'create' button next to 'filter:', and setting 'strand does match +' (for the positive strand)." Can you please clarify? Do we download the knownCanonical and knownGene tables separately and filter genes by hand, or is there a way to retrieve only the information from knownGenes that overlaps with knownCanonical? Thank you, ---Karmella -- Karmella A. Haynes, Ph.D. Assistant Professor School of Biological and Health Systems Engineering Arizona State University 501 E. Tyler Mall, ECG 346 Tempe, AZ 85287 E-mail: [email protected]<mailto:[email protected]> Website: haynes.lab.asu.edu _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
