Figure 2. DNA copy number alteration across chromosome 8 by array CGH. (a) DNA copy number profiles are illustrated for cell lines containing different numbers of X chromosomes, for breast cancer cell lines, and for breast tumors. Breast cancer cell lines and tumors are separately ordered by hierarchical clustering to highlight recurrent copy number changes. The 241 genes present on the microarrays and mapping to chromosome 8 are ordered by position along the chromosome. Fluorescence ratios (test/reference) are depicted by a log2 pseudocolor scale (indicated). Selected genes are indicated with color-coded text (red=increased, green=decreased, black=no change, gray=not well-measured) to reflect correspondingly altered mRNA levels (observed in the majority of the subset of samples displaying the DNA copy number change). The map positions for genes of interest that are not represented on the microarray are indicated in the row above those genes represented on the array. (b) Graphical display of DNA copy number profile for breast cancer cell line SKBR3. Fluorescence ratios (tumor/normal) are plotted on a log2 scale for chromosome 8 genes, ordered along the chromosome.