PAGE 5 OF 11 Nucleic Acids Research, 2009, Vol. 37, No. 12 e89 Figure 2. Comparison of methylation analysis of cell lines. (A–C) shows the comparison of a normal ﬁbroblast used to produce representations from two separate aliquots of DNA and the representations were analyzed and the intensity compared to each other by scatter plot; the intensities of each being on one and the other axis, and the correlation calculated: (A) being replicate hybs, (B) being technical replicates and (C) being biological replicates. (D) The comparison of the breast cancer cell line SKBR3 and the normal female ﬁbroblast cell line as a scatter plot of the intensities from the SKBR3 experiment as the y-axis and the intensities of chp-skn-1 on the x-axis, and the correlation shown. (E) An example of bisulﬁte validation for a fragment found methylated in the tumor and not in the normal at a CpG island at chr 9:2197965–21980065, which lies upstream of the p14 gene. The original data showing the ratio diﬀerences is shown with the position of the fragment. To the right is the electropherogram identifying a region of cytosines that do not convert and at the bottom is a short table identifying the genomic position and number of McrBC site. (F) shows data for the cell line Huh7 compared to the normal cell line chp-skn-1 for the p16 gene CpG island graphed by genomic position. The x-axis is the genomic position of the probes and the y-axis is the ratio of two experiments, blue being chp-skn-1 and orange being Huh7. Inset above is shown is the relation of the transcript and inset below is the relation of the CpG island to the probes.