Fig. 2

Estimating proportions of DNA methylation modifications. a Scatter plot representations of the observed changes in 5mC levels (estimated over three replicates) between wild-type and Tet2 knock-down cells across all the cytosines in the 14 genomic loci studied. The estimated posterior means and their standard deviations are illustrated. The cytosines are grouped based on their sequence context. The coloring of the circles depicts the estimated 5hmC levels in v6.5. b The estimated posterior means of 5hmC and 5mC levels from three replicates per condition are depicted in the bar charts (top panel). Only the cytosines in a CpG context and the designed amplicon are depicted. Read density profiles from affinity-based measurements of 5hmC and 5mC levels across the locus chr16:92,644,158-92,645,157 are shown (bottom panel). c Scatter plot representations of 5hmC levels estimated using CMS-IP and BS-/oxBS-seq (top panel) and 5mC using MeDIP and BS-/oxBS-seq (bottom panel) measurements. The conditions are set apart by the color. Random jitter has been added to the scatter plot points to avoid overlapping points. d A pair-wise comparison between the Lux and MLML replicate-specific 5hmC level estimates. Only the cytosines in a CpG context are considered. The Pearson’s correlation coefficients are shown