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

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==Entry title==
==Entry title==
* Insert content here...
* 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




Revision as of 13:40, 29 January 2012

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Entry title

  • 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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