<p>A) Dormancy score analysis in breast cancer cell lines. The cell lines are ordered by dormancy scores (low to high from left to right). The rows correspond to genes and the columns represent cell lines. Expression levels for positive dormancy genes (upregulated genes - top section) and negative dormancy genes (downregulated genes - bottom section) were clustered by a hierarchical clustering algorithm. The colors represent log<sub>2</sub> fold change compared to the average from −2.5 (blue, below average) to +2.5 (red, above average) with white as the average value. A, B, and L stand for Basal A, Basal B, and Luminal classifications, respectively. B) Correlation of cell line dormancy scores with proliferation indices from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035569#pone-0035569-t001" target="_blank">Table 1</a> of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035569#pone.0035569-Kenny1" target="_blank">[9]</a> with ER- lines plotted as squares and ER+ lines plotted as diamonds. Straight line fits of ER- (blue, Spearman correlation coefficient r = .027) and ER+ (red, r = −0.76) cell lines are plotted. The ER status of HCC1500 is unclear (ATCC indicates it as ER+ while it is ER- by gene expression and Western blot in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035569#pone.0035569-Neve1" target="_blank">[8]</a>) and it was not used in the analysis. MDA-MB-231 (large orange square), MCF7 (large green diamond) and T47D (large yellow diamond) are identified. C) Patient tumor analysis. The four clinical studies were clustered as in A. In the ER status bar, ER status is indicated by black (ER+), blue (ER−) or white (not determined) bars. The two genes for which probes were not present in the van de Vijver et al. data set are represented by gray bars. D) Comparison of clustering of cell lines and patient data. Top: Positive dormancy genes that are upregulated in high dormancy score cell lines or patients. Bottom: Negative dormancy genes that are up regulated in low dormancy score cell lines or patients.</p
