Execute the R Scripts
Last updated
Last updated
ls -la ~/Scripts/Figure1.pdf
Figure 1. Line plots showing the DNA methylation in H1 and IMR90 along the chromosomal length.
ls -la ~/Scripts/Figure2*.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.
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
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.
ls -la ~/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.
