Execute the R Scripts

Plot Overview

cd ~/Scripts
wget --no-check-certificate https://raw.githubusercontent.com/ycl6/MethylationWorkshop2014/master/R/plot_overview.R

Rscript --vanilla plot_overview.R

ls -la ~/Scripts/Figure1.pdf

# Console output

-rw------- 1 s00yao00 s00yao00 119244 2014-12-20 21:04 /home/s00yao00/Scripts/Figure1.pdf

Figure 1. Line plots showing the DNA methylation in H1 and IMR90 along the chromosomal length.

Plot Locations

cd ~/Scripts
wget --no-check-certificate https://raw.githubusercontent.com/ycl6/MethylationWorkshop2014/master/R/plot_locations.R

Rscript --vanilla plot_locations.R

ls -la ~/Scripts/Figure2*.pdf

# Console output

-rw------- 1 s00yao00 s00yao00     6025 2014-12-20 21:05 /home/s00yao00/Scripts/Figure2a.pdf
-rw------- 1 s00yao00 s00yao00 14745034 2014-12-20 21:05 /home/s00yao00/Scripts/Figure2b.pdf
-rw------- 1 s00yao00 s00yao00  1522371 2014-12-20 21:05 /home/s00yao00/Scripts/Figure2c.pdf

Figure 2A. Bar plots showing the DNA methylation levels within the five types of genomic regions. Majority of the differences between H1 and IMR90 occur in introns and intergenic regions that have between 20% to 80% DNA methylation levels.

Figure 2B. H1 is more methylated than IMR90 in many regions (arrows). The DNA methylation pattern of X chromosome is also different between H1 (male) and IMR90 (female), especially in promoter regions (circle). This is due to the fact that female possesses two X chromosomes and one is randomly and permanently inactivated by DNA methylation.

Figure 2C. The 5’ UTRs are more hypomethylated compared to the 3’ UTRs.

Plot Regulatory Sites

cd ~/Scripts
wget --no-check-certificate https://raw.githubusercontent.com/ycl6/MethylationWorkshop2014/master/R/plot_regulatory.R

Rscript --vanilla plot_regulatory.R

H1 vs. IMR90	<20%	20%-50%	50%-80%	>80%
<20%	67.6998	2.8443	0.3241	0.0000
20%-50%	3.6164	7.3603	3.9114	0.0692
50%-80%	0.8631	2.8006	8.1943	0.9943
>80%	0.0291	0.0728	0.6118	0.6082

Table 3. Frequency table showing the CpG Island methylation levels in H1 and IMR90.

ls -la ~/Scripts/Figure3.pdf

# Console output

-rw------- 1 s00yao00 s00yao00 13663 2014-12-20 21:06 /home/s00yao00/Scripts/Figure3.pdf

Figure 3A. Majority of the DNA methylation pattern between the two cell lines across all TFBS are similar, with a few exceptions such as c−Jun, GR, and p300. You may use t-test to test the significance of the difference between the two sample means.

Figure 3B. Most of the repeated sequences in IMR90 are more hypomethylated except SINE elements.

Plot HMR and PMD Coverage

cd ~/Scripts
wget --no-check-certificate https://raw.githubusercontent.com/ycl6/MethylationWorkshop2014/master/R/plot_hmr_pmd.R

Rscript --vanilla plot_hmr_pmd.R

ls -la ~/Scripts/Figure4.pdf

# Console output

-rw------- 1 s00yao00 s00yao00 53267 2014-12-20 21:06 /home/s00yao00/Scripts/Figure4.pdf

Figure 4A. Both the HMRs and PMDs are longer in IMR90. The PMD of IMR90 are approximately 50 times longer than that in H1 (PMD median length: ~ 320 Kb in IMR90 and ~6 Kb H1)

Figure 4B. The H1-specific HMRs are much shorter than other kinds of HMRs. The H1-specific PMDs are also very short compared to PMDs specific to IMR90. This data is consistent with that observed in Figure 4A.