CpG Island Mapping by Epigenome Prediction
Figure 5
Performance of the Combined Epigenetic Score Compared between CpG Island Maps That Use Different Repeat-Exclusion Strategies
This figure plots the precision (i.e., the percentage of experimentally supported bona fide CpG islands among all selected CpG islands) and the true positive rate (i.e., the percentage of experimentally supported bona fide CpG islands that are selected) over the total number of cases predicted as bona fide CpG islands, for any valid threshold on the combined epigenetic score. Evaluation criteria are absence of DNA methylation (A) and presence of promoter activity as indicated by experimentally determined transcription start sites (B). The three scales on top of each plot display the score thresholds that correspond to the number of CpG islands selected. Dashed lines show the three thresholds that were used to derive the final bona fide CpG island maps on the basis of the GGM dataset. Numbers on the x-axis are significantly lower in (A) than in (B) because of the fact that the DNA methylation dataset covers only a random sample of unmethylated and methylated CpG islands, while the promoter activity dataset covers essentially all nonrepetitive CpG islands genome-wide.