Haynes Lab:Notebook/Synthetic Biology and Bioinformatics for Predictable Control of Therapeutic Genes/2012/01/29

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  • To elaborate on the description that was given on the 25th

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



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