Extended Data Figure 6: Clonal analysis in MCF7 and HepG2 cancer cell lines.

a, HepG2 pattern clusters of low methylation regions. Data for one clonal and one non-clonal population are shown. Visualization is as in Figs 1 and 2. b, Annotation of low methylation HepG2 pattern clusters. c, High methylation HepG2 pattern clusters. d, Intermediate methylation pattern clusters. Overall the HepG2 methylome is defined by a large set of intermediate methylation regions. e, Distribution of replication time (K562 Repli-Seq) for HepG2 pattern clusters. Clusters with intermediate methylation show a clear bias towards late replication. f, Pattern clusters of low methylation regions, comparing non-clonal and clonal MCF7 populations. MCF7 methylomes are saturated for high methylation, so persistent low methylation clusters are not observed. g, Annotation of low methylation clusters. High noise regions are enriched for H3K27me3 ES-cell occupancy. h, High methylation pattern clusters. i, Intermediate methylation MCF7 pattern clusters. Note that since only one clonal population is analysed the number of common partial patterns cannot be large. j, Distribution of replication times (K562 Repli-Seq data) on all MCF7 classes.