Figure 2. Cluster analysis using the "intrinsic" gene subset. Two large branches were apparent in the dendrogram, and within each of these two branches, smaller branches were identified for which common biological themes could be inferred. The branches are colored accordingly (basal-like = orange, Erb-B2 positive = pink, normal breast-like = light green, and luminal epithelial/ER+ = dark blue). a, experimental sample associated cluster dendrogram. The small black bars beneath the dendrogram identify the 17 pairs that were matched by this hierarchical clustering, while the larger green bars identify the positions of the three pairs that were not matched by the clustering. b, Scaled-down representation of the "intrinsic" cluster diagram (the complete "intrinsic" cluster diagram is Supplementary Information Figure 5). c, Luminal epithelial/ER gene cluster. d, Erb-B2 overexpression cluster. e, basal epithelial cell associated cluster containing keratins 5 and 17. f, a second basal epithelial cell enriched gene cluster.