Figure 1

Differences in DNA methylation patterns across the genome distinguish ovarian tissues by stage (see Additional Files 2 and 3 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.