Table 2. CpG dimer-level correlations between differential values for all bisulfite sequencing library pairs.
Pearson correlation values between WGBS, RRBS, and MREBS differential CpG dimer-level methylation estimates (EARLY—ESC), as well as differential read counts between all CpG dimers with at least two MREBS reads within a surrounding 1kb window. Red intensity signifies the strength of a positive correlation, while blue intensity signifies the strength of the anti-correlation.
| CpG dimer-level differential methylation using conversion-based estimates * | Differential MREBS read counts within 1kb windows around CpG dimers ** | |||||||
| WGBS | RRBS | MREBS | ||||||
| Rep1 | Rep2 | Rep1 | Rep2 | |||||
| CpG dimer-level differential methylation using conversion-based estimates * | WGBS | 1.00 | 0.63 | 0.55 | 0.56 | -0.34 | -0.34 | |
| RRBS | 0.63 | 1.00 | 0.64 | 0.64 | -0.51 | -0.52 | ||
| MREBS | Rep1 | 0.55 | 0.64 | 1.00 | 0.64 | -0.35 | -0.35 | |
| Rep2 | 0.56 | 0.64 | 0.64 | 1.00 | -0.34 | -0.34 | ||
| Differential MREBS read counts within 1kb windows around CpG dimers ** | Rep1 | -0.34 | -0.51 | -0.35 | -0.34 | 1.00 | 0.87 | |
| Rep2 | -0.34 | -0.52 | -0.35 | -0.34 | 0.87 | 1.00 | ||
* For CpG dimers with 5X coverage in both cell lines
** For windows with at least two MREBS reads in at least one cell line