Figure 1. Hierarchical clustering analysis for all genes across all arrays. A representation of the variation in expression of 1550 genes in the 38 tumors and three normal samples is shown at the left. The right panel depicts the detailed sample dendrogram in which three primary tumors and their associated renal vein/ vena caval thrombi are designated on the dendrogram by branches with filled circles at the ends. Each row represents a single gene. Each column represents a single sample. The hierarchical clustering algorithm organizes the experimental samples only on the basis of overall similarity in their gene expression. Green squares indicate transcript levels below the mean; black squares, transcript levels equal to the mean; red squares, transcript levels greater than the mean; gray squares, technically inadequate or missing data. Gene filtering criteria were for four-fold variation from the normalized mean and at least 80% well measured spots. Colored bars adjacent to the clustering table indicate the position of the enlarged images. The color of the bar indicates the type of sample in which the cluster of genes is expressed. Green – papillary gene cluster; Blue – normal gene cluster; Orange – chromophobe/oncocytoma gene cluster; Red – conventional clear cell carcinoma gene cluster. Selected gene names are shown.