User:David K. Barclay/Notebook/Controlling Pancreas Cell Fate Using Transcription Factors/2014/06/23: Difference between revisions

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==Entry title==
==Bioinformatics- Promoter/H3K27me3 mark crosses in excel==
* Insert content here...


===GALAXY Procedure===
# Download .bed data from lab's backfile and upload to GALAXY (usegalaxy.org). Toolbar left > Get Data > Upload File > Select .bed file > File Format: Interval, Genome: hg18 > Execute.
# Upload refseq promoters (hg18) in same fashion as .bed data if stored on hard drive.
# Intersect promoter with crosses: Toolbar left > Operate on Genomic Intervals > Intersect > Return: Overlapping Intervals, of: methyl-histone data, that intersect: promoters, for at least: 1 bp > Execute.
# Once new data analysis is run, regions should display under title for analysis. Enter all crosses data into excel spreadsheet for analysis.
# Intersect new cross data with all other crosses made. This will give regions that both cell experiments contain. For example, a cross for cell experiments A1 and B1 will contain all regions that have histone methylation in both data.
===Excel Procedure===
# Create a table consisting of all cell experiments from alpha cells to exocrine cells on both the x and y axis (Figure 1).
# In each cross (e.g. A1 cross B1) mark down the number of regions similar. Data will come from previous GALAXY crosses.
# Heat map analysis using conditional formatting on Excel. Darker numbers = near maximum, lighter numbers = near minimum.
* Crosses between H3K27me3 data (Bramswig et al. 13)and reference promoters were done in Excel. They show number of genes hypothetically controlled by the histone methylation mark.
[[Image:Bramswig Crosses.png]]
*Figure 1
*Crosses revealed around 4950 promoters were controlled in alpha cells. Heat map analysis indicates that alpha cells are more heavily affected by H3K27me3 marks than beta cells. Crosses between alpha/beta cell histone methylation (i.e. A1-3 cross B1-3 on the table) show there are around 1000 genes that are associated with the methyl-histone mark in alpha cells but not in bet cells.


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Revision as of 12:24, 11 July 2014

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Bioinformatics- Promoter/H3K27me3 mark crosses in excel

GALAXY Procedure

  1. Download .bed data from lab's backfile and upload to GALAXY (usegalaxy.org). Toolbar left > Get Data > Upload File > Select .bed file > File Format: Interval, Genome: hg18 > Execute.
  2. Upload refseq promoters (hg18) in same fashion as .bed data if stored on hard drive.
  3. Intersect promoter with crosses: Toolbar left > Operate on Genomic Intervals > Intersect > Return: Overlapping Intervals, of: methyl-histone data, that intersect: promoters, for at least: 1 bp > Execute.
  4. Once new data analysis is run, regions should display under title for analysis. Enter all crosses data into excel spreadsheet for analysis.
  5. Intersect new cross data with all other crosses made. This will give regions that both cell experiments contain. For example, a cross for cell experiments A1 and B1 will contain all regions that have histone methylation in both data.

Excel Procedure

  1. Create a table consisting of all cell experiments from alpha cells to exocrine cells on both the x and y axis (Figure 1).
  2. In each cross (e.g. A1 cross B1) mark down the number of regions similar. Data will come from previous GALAXY crosses.
  3. Heat map analysis using conditional formatting on Excel. Darker numbers = near maximum, lighter numbers = near minimum.
  • Crosses between H3K27me3 data (Bramswig et al. 13)and reference promoters were done in Excel. They show number of genes hypothetically controlled by the histone methylation mark.


  • Figure 1
  • Crosses revealed around 4950 promoters were controlled in alpha cells. Heat map analysis indicates that alpha cells are more heavily affected by H3K27me3 marks than beta cells. Crosses between alpha/beta cell histone methylation (i.e. A1-3 cross B1-3 on the table) show there are around 1000 genes that are associated with the methyl-histone mark in alpha cells but not in bet cells.


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