Table 3.
Summary of temporal trend (β-scale) in CpG site methylation, by genomic location and probe type.1
| Nonsex chromosomes
|
X chromosome
|
|||||
|---|---|---|---|---|---|---|
| Percent loci with significant trend
|
Percent loci with significant trend
|
|||||
| Location/probe type | N | Negative trend | Positive trend | N | Negative trend | Positive trend |
| All CpG loci | 472665 | 1.86 | 1.54 | 11215 | 1.84 | 1.64 |
| Enhancer | 101663 | 1.83 | 1.79 | 629 | 1.75 | 1.91 |
| Known DMR2 | 36053 | 1.91 | 1.29 | 1231 | 1.54 | 1.62 |
| Location with respect to CpG island: | ||||||
| CpG Island | 145571 | 1.91 | 1.31 | 4272 | 2.01 | 1.17 |
| Shore3 | 108839 | 1.93 | 1.50 | 2837 | 1.97 | 1.55 |
| Shelf3 | 45790 | 1.86 | 1.70 | 1138 | 1.85 | 1.76 |
| Functional location: | ||||||
| TSS1500 | 81267 | 1.94 | 1.44 | 2777 | 2.02 | 1.76 |
| TSS200 | 60005 | 1.88 | 1.38 | 2441 | 2.17 | 1.11 |
| 5′UTR | 62975 | 1.88 | 1.42 | 2401 | 2.25 | 1.71 |
| 1st Exon | 37656 | 1.93 | 1.34 | 1635 | 2.32 | 1.59 |
| Body | 172068 | 1.86 | 1.58 | 2893 | 1.69 | 1.56 |
| 3′UTR | 19174 | 1.83 | 1.60 | 513 | 1.95 | 3.31 |
| Location by probe type: | ||||||
| Infinium I | 132039 | 1.55 | 1.59 | 3042 | 1.94 | 1.15 |
| Infinium II | 340626 | 1.99 | 1.52 | 8173 | 1.80 | 1.82 |
1
All estimates are adjusted for cell-type composition. Δβ is estimated as twice the between-person standard error (β-scale).
2
DMR: differentially methylated region; TSS: transcription start site; UTR: untranslated region.
3
Shores: up to 2 kb from CpG islands; shelves: from 2 to 4 kb from CpG islands.