Confirmation of expression measurements by real-time RT-PCR. GeneChip median expression for 46 genes from Table 3 within one sample was adjusted to 100 RLU. Then, all measurements were median centered for each gene. Hierarchical clustering algorithm was applied to median normalized expression data of 46 genes from 39 tumor samples from training and test cohorts. Hierarchical clustering presents the clustered samples in columns and the clustered 46 genes in rows. A color representation of gene expression levels is shown with the scale on the left side (pCR represented in green, NC represented in red). Clustering of the data was performed according a correlation analysis with an average distance determination. The threshold Ct values obtained in real-time RT-PCR were converted into an arbitrary RNA-copy number Ct value of 24, which was then empirically settled to 106 RNA copies per well. These measurements were median centered, as for microarray data. All data for samples and genes were ordered according to the hierarchical structure of the microarray data set in Fig. 3A for Affymetrix platform.