Figure 4

Predicted DMBs (DMBs predicted to have methylation difference over 0.5 from mixture reads by MethyIPurify) are compared with true DMBs (DMBs inferred from BS-seq reads in two separate cell lines) in HCC and HMEC cell lines. (a) Overlap between predicted (from mixture, red) and true (blue) DMBs in the mixture of HCC1954 (70%) and HMEC (30%). (b, c) Correlations of predicted and true methylation levels in normal (b) and tumor cell line (c) for qualifying bins. (d) An example of differentially methylated region between HCC and HMEC cell lines. Each point represents one qualifying bin of length 300 bp. HMEC.t and HCC.t are true methylation profiles in this region, while HMEC.p and HCC.p are predicted methylation profiles from mixture reads. (e) Correlation of predicted and true methylation differences. (f) DMB prediction sensitivity and correlation of methylation between predicted and true differential methylation at different mixing ratio of the two cell lines.