From: Human-macaque comparisons illuminate variation in neutral substitution rates
Class of elements | Short description | Conservation based | Reference | Correlation coefficient | Partial correlation coefficient |
---|---|---|---|---|---|
phyloHMM (P) | Predicted functional elements; highly conserved non-exonic sequences identified by phyloHMM | Yes (17 vertebrate species) | [52] | -0.32 | -0.38 |
ESPERR-RP (P) | Predicted regulatory elements; non-exonic sequences with high regulatory potential, as measured by the ESPERR-RP score | Yes (7 mammalian species) | [39] | -0.24 | -0.30 |
Enhancers (P) | Predicted enhancers; non-exonic sequences under strong constraint in human-rodent comparisons | Yes (human, mouse, rat) | [38,48] | -0.06 | -0.22 |
CTCF-binding sites (P) | Predicted CTCF binding sites; identified by single sequence motif finding methods | No | [41] | -0.12 | -0.10 |
CTCF-binding sites (E) | Experimentally mapped CTCF binding sites | No | [41] | -0.20 | -0.08 |
ER binding sites (E) | Experimentally mapped estrogen receptor binding sites | No | [42] | -0.14 | -0.09 |
RNA polymerase II binding sites (E) | Experimentally mapped RNA polymerase II binding sites | No | [42] | -0.11 | 0.01 |