Figure 2

Variation in gene expression as a function of sample-type. A & B. Samples plotted as a function of their loading for the primary axes of variation in gene expression as identified by principal components analysis. A. Samples plotted on the primary (PC-1) and secondary (PC-2) axes of variation. PC-1 accounts for 91.5% of the variation in gene expression and PC-2 accounts for 4.1% of the variation. The primary axis of variation in gene expression organizes the samples according to whether they are from tumor or adjacent normal tissue. B. Samples plotted on the primary and tertiary (PC-3) aces of variation. PC-3 accounts for 1.5% of the variation in gene expression. The tertiary axis of variation in gene expression organizes the tumor samples according to their Fuhrman grade. C. Hierarchical clustering of the samples in which the height of the vertical lines are proportional to the degree of dissimilarity between nodes. In all three panels the samples are labeled with the sample ID and the symbols are coded to represent sample type (large symbols represent tumor samples, small symbols represent normal tissue adjacent to the tumor), the Fuhrman grade of the tumor (filled symbols represent grade I, shaded symbols represent grade II, open symbols represent grade III), and whether the tumor had penetrated the renal capsule (round symbols represent penetrant tumors).