Differences in DNA methylation patterns across the genome distinguish ovarian tissues by stage (see Additional Files
for sample histopathology and the list of sequences used in clustering). a) The 659 CpG-rich clones with differential methylation between any two tumor stages were used in hierarchical clustering by Pearson correlation and average linkage. Each CpG-rich clone is represented by one bar and colored by their average methylation relative to the median of the ten normal samples; hypermethylation is shown in red and hypomethylation shown in blue. Horizontally aligned black bands mark the position of specific ranks of clones: Rank 1, the clone sequence lies within 0.5 kb of the transcription start of a known gene; Rank 2, the clone lies within 1 kb of transcription start; Rank 3, the clone lies within 2 kb of transcription start; Rank 4, the clone lies >2 kb from transcription start; Satellites, probes containing satellite repeats; Alu, probes of which the clones consist of >25% Alu sequence. b) The same 659 CpG-rich clones are graphed by tumor stage. Each CpG-rich clone is represented by one line. Lines are colored by their average methylation in Stage IV; blue indicates loss of methylation, and red indicates gain of methylation, relative to the median of the ten normal samples.