Figure 1. Variation in expression of 1753 genes in 84 experimental samples. In this illustration, the data are presented in a matrix format, with each row representing a single gene, and each column representing an experimental sample. The ratio of the abundance of transcripts of each gene, in each sample, to the median abundance of the gene's transcript among all the cell lines (left panel) or to its median abundance across all tissue samples (right panel) is represented by the color of the corresponding cell in the matrix. Green squares represent transcript levels below the median; black squares represent transcript levels equal to the median; red squares represent transcript levels greater than the median; gray squares indicate technically inadequate or missing data. The color saturation reflects the magnitude of the ratio relative to the median for each set of samples (see scale at bottom left and Supplementary Information Figure 3 for the complete cluster diagram). a, Dendrogram representing similarities in the expression patterns between experimental samples. All "before and after" chemotherapy pairs that were clustered on terminal branches are highlighted in red; the two primary tumor/lymph node metastasis pairs are highlighted in light blue; the three clustered normal breast samples are highlighted in light green. The branches representing the four breast luminal epithelial cell lines are displayed in dark blue; breast basal epithelial cell lines are displayed in orange, the endothelial cell lines in dark yellow, the mesynchemal-like cell lines in dark green, and the lymphocyte-derived cell lines in dark red. b, Scaled down representation of the 1753 gene cluster diagram; the colored bars to the right identify the locations of the inserts displayed in 1c-j. c, endothelial cell gene expression cluster. d, stromal/fibroblast cluster. e, breast basal epithelial cluster. f, B-cell cluster. g, adipose-enriched/normal breast. h, macrophage. i, T-cell. and j, breast luminal epithelial cell.