Fig. 3.

HCGDs. (A) The COCAD assay. Shown are the observed (red) and predicted (green) number of human or chimp CpGs that are not conserved in a 20-kb sliding window at part of chromosome 5p. The prediction is based on the M-score of each CpG and can vary significantly depending on the sequence context of the CpG. An anomalously low CpG divergence at the Iroquois homeobox protein 2 (IRX2) and CEI genes is shown (Center), and the difference between observed and predicted divergence is transformed to a statistical score (blue, Lower). Genomic loci with COCAD scores lower than −5 are defined as HCGDs. (B) HCGDs are located near genes for key developmental regulators. Of the 134 HCGDs that are near characterized genes, 128 are near genes related to regulation of developmental processes. (C) Chromosomal distribution of HCGDs (blue) and PRC2 domains (red).