Table 1.
Spatial relationships between genomic intervals of top DMRs and selected genomic features
| Hypomethylated (n = 507) | Hypermethylated (n = 345) | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Statistical concept | Interpretation | SINE | LINE | LTR | DNAt | snRNA | Low | CpGi | Genes | SINE | LINE | LTR | DNAt | snRNA | Low | CpGi | Genes |
| Reference population | Number entities within each class | 1769839 | 1480369 | 708210 | 456948 | 4285 | 367822 | 27718 | 23033 | 1769839 | 1480369 | 708210 | 456948 | 4285 | 367822 | 27718 | 23033 |
| Relative KS p-value | Relative relationship between interval midpoints | <0.05 | n.s. | n.s. | n.s. | n.s. | <0.1 | n.s. | <0.1 | <0.0001 | <0.01 | n.s. | n.s. | n.s. | <0.05 | n.s. | n.s. |
| Type of relationship | Positive | – | – | – | – | Negative | – | Positive | Positive | Negative | – | – | – | Negative | – | – | |
| Jaccard Measure p-value | Ovelaps between intervals | < 0.0001 | <0.01 | <0.1 | n.s. | n.s. | <0.05 | n.s. | <0.0001 | <0.0001 | <0.001 | n.s. | n.s. | n.s. | n.s. | n.s. | <0.1 |
| Type of overlap | Positive | Negative | Positive | – | – | Negative | – | Positive | Positive | Negative | – | – | – | – | – | Positive | |
Test statistics were obtained using the GenometriCorrelation package in R/Biocunductor. For more information about the different tests see Favorov et al. 2012. Both KS (Kolmogorov-Smirnov) and Jaccard Measure p-values were obtained by permuting the obeserved results 10 000 times over the human genome. SINE Short interspersed nuclear elements, LINE Long interspersed nuclear elements, LTR Long terminal repeats, DNAt DNA transposon, snRNA Short nuclear RNA repeats, Low Low complexity DNA, CpGi CpG island