Nucleic Acids Research, 2007, Vol. 35, No. 20 6803 Figure 4. (a) CG clusters (white bars) overlap more refSeq transcription start sites than the CpG island annotations of the UCSC genome browser (black bars). CG clusters overlap the presumed promoters of a substantially higher proportion of genes overall (left), including both housekeeping and tissue-speciﬁc genes. In panel (b) we add in (in black) the number of loci that do not overlap refSeq promoters (white) to demonstrate the ‘false positive’ rate for the categories shown in panel (a), as well as the 350 201 CpG islands found when all genomic sequence is tested without removing repetitive elements and the CG clusters that are not deﬁned by transposable elements. The positive predictive value for CpG islands and CG clusters (bold) are also shown, quantifying the relative performance of each of these annotations. CpG islands have been used as a component of algorithms for predicting promoters in the genome (6), CG clusters should oﬀer a more powerful resource for this and comparable purposes. We tested the relative ability of CG clusters to detect hypomethylated sites by performing the HELP assay (12) on human embryonic stem cells and CD34+ hematopoi- etic stem and progenitor cells. A microarray representing HpaII-ampliﬁable fragments located near transcription start sites in the human genome was used for two biological replicates of each cell type. While similar proportions of loci at CpG islands and at CG clusters