Hierarchical clustering of 89 breast tumor samples (sample set A). Each column represents a tumor sample, and each row represents a different gene probe set. The relative expression level of the genes in the samples is indicated by a gradient of color, with blue representing expression levels below the mean and red representing expression levels above the mean. The tumors are clustered in the dendrogram at the top, and the genes are clustered in the dendrogram down the side. Tumors and genes appearing next to each other are more similar in expression pattern. The pathologic data for each tumor sample is represented by the color bars below the tumor dendrograms: dark blue, modified Bloom-Richardson grade III; light blue, modified Bloom-Richardson grade I or II; dark green, ER and PR positive; light green, ER and PR negative; dark purple, Her-2 overexpressed (3+); light purple, Her-2 nonoverexpressed. The tumor clusters showing the highest levels of Skp2 expression and the gene clusters that include the Skp2 gene are highlighted in orange. (a) Hierarchical clustering of 89 tumors for 2,130 filtered genes. (b) Clustering of 89 tumors to demonstrate relative expression of 41 selected genes, including cell cycle regulatory genes (e.g., cyclins, Cdks, Cks1, Cks2, PCNA, p16), keratins, hormone receptors (e.g., ERα, ERβ, ERRα, androgen receptor), ER-associated genes (e.g., HNF3, TFF3, GATA3, LIV-1), Her-2 amplicon genes (e.g., Her-2, PPAR-binding protein, MLN64, GRB7), and genes associated with the basal-like tumor subgroup (e.g., UDP-N-Ac-galactosamine, chitinase 3-like 2, P-cadherin, AC133/prominin-like 1, HDGF).