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Table 4 Associations between human-macaque neutral substitution rates and frequencies of various classes of functional elements

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
  1. Pearson's correlation and partial correlation coefficients. The substitution rates are estimated from all sites in ancestral repeats (without requiring orthology to mouse, rat, dog and cow) for each of 2,270 windows of size1 Mb.