Figure 3

The methylation profile, gene expression profile and DNA copy number variation of loci on Chromosome 1. Chromosome 1 was selected as a representative of the chromosome set. Similar information for the other chromosomes is presented in Additional file 8. A diagram of chromosome 1 is located in the middle. The common fragile sites are symmetrically indicated with thin solid black lines (the rare fragile sites marked with blue). The corresponding data for MCF-7 and MDA-MB-231 are presented to the left and the right sides of the chromosome, respectively. The DNA copy number variation, gene expression and methylation status are shown consecutively. For DNA copy number variation, green, red and mild yellow mean amplification, deletion and no change, respectively. The length of the red bars that are vertical to the chromosome indicates the expression level for the corresponding genes. The length of bars located the most outside of the figure represents the methylation extent for the corresponding MluI sites on the chromosome. Blue indicates tags mapped with high confidence (mapping quality more than 20) and yellow represents all mapped tags.