User:David K. Barclay/Notebook/Controlling Pancreas Cell Fate Using Transcription Factors/2014/04/12: Difference between revisions

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| 20 || KCNQ2 || 62031317 || 62031817 || 4
| 20 || KCNQ2 || 62031317 || 62031817 || 4
|}
|}
* <font color=red>Dr. Haynes: What does "Signal" mean in this table?</font>


===Table Browser Protocol (UCSC)===
===Table Browser Protocol (UCSC)===
Line 33: Line 35:
# Go to UCSC Table Browser http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=356574357
# Go to UCSC Table Browser http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=356574357
# Clade to Mammal, Genome to Human, Assembly to Mar. 2006 (hg18)
# Clade to Mammal, Genome to Human, Assembly to Mar. 2006 (hg18)
## <font color=red>Dr. Haynes: Try Feb. 2009 (hg19)</font>
#Track to UW Histone
#Track to UW Histone
#Region defined as TSS+250 and TSS-250 above
## <font color=red>Dr.  Haynes: What did you set '''table''' to?</font>
#Region defined as TSS+250 and TSS-250 above. Format of Defining region as:
 
 
{| class="wikitable" style="width: 300px;"
|- valign="top"
|chrX || TSS-250  ||  TSS+250 ||  gene name
|-
|chr13 ||  28493908 || 28494408 || PDX1
|}
 
 
#Output format to "selected fields from primary and related tables." Click get output
#Output format to "selected fields from primary and related tables." Click get output
#Select: chrom, chromStart, chromEnd, name and signalValue
#Select: chrom, chromStart, chromEnd, name and signalValue
<font color=red>Dr. Haynes: When I set "table" to H1-hESC H3K27m3 (wgEncodeBroadHistoneH1hescH3k27me3StdPk), I got the following output for PDX1
{| class="wikitable" style="width: 400px;"
|- valign="top"
|#chrom || chromStart  ||  chromEnd ||  name || signalValue || [Gene]
|-
|chr13 ||  28468953 || 28571921 || . || 52.9896 || PDX1
|}
</font>


===Results===
===Results===

Revision as of 14:47, 15 April 2014

Cell Fate Switch by Synthetic Transcription Factors <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>

Promoters Bioinformatics

H3K27me3 markers TSS sites

  • Workflow Part 1
H3K27me3 Markers TSS sites
Chromosome Gene TSS+250 TSS-250 Signal
13 PDX1 28493908 28494408 85.24
6 GLP1R 39016307 39016807 20.72
8 MAFA 144509980 144510480 140.76
5 PCSK1 95725790 95726290 1
12 IAPP 21525552 21526052 2
20 KCNQ2 62031317 62031817 4
  • Dr. Haynes: What does "Signal" mean in this table?

Table Browser Protocol (UCSC)

  • Workflow Part 2
  1. Go to UCSC Table Browser http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=356574357
  2. Clade to Mammal, Genome to Human, Assembly to Mar. 2006 (hg18)
    1. Dr. Haynes: Try Feb. 2009 (hg19)
  3. Track to UW Histone
    1. Dr. Haynes: What did you set table to?
  4. Region defined as TSS+250 and TSS-250 above. Format of Defining region as:


chrX TSS-250 TSS+250 gene name
chr13 28493908 28494408 PDX1


  1. Output format to "selected fields from primary and related tables." Click get output
  2. Select: chrom, chromStart, chromEnd, name and signalValue


Dr. Haynes: When I set "table" to H1-hESC H3K27m3 (wgEncodeBroadHistoneH1hescH3k27me3StdPk), I got the following output for PDX1

#chrom chromStart chromEnd name signalValue [Gene]
chr13 28468953 28571921 . 52.9896 PDX1

Results

No results found, none of genes found with UW histone markers.


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