FIGURE 3

Clustering of the 439 discriminatory genes. (a) Hierarchical clustering was performed using the average linkage method with Euclidean distance as the distance function. Changes in the expression levels (T-values) are illustrated using a color-coding, where red corresponds to increasing expression levels, green to decreasing expression level, and black to stable expression during the time series. (b) Clustering of the 439 genes was performed using the SOM algorithm (Kohonen, 2001; Hautaniemi et al., 2003b) using a toolbox made by Vesanto et al. (2000). The unified-distance matrix (U-matrix) and component plane representation are shown. The U-matrix illustrates the presence of two major clusters of genes (shown in blue) that are separated by a row of red-shaded map units. The colored component planes for each cell line indicate that the expression patterns of these major clusters in the amplified cell lines are markedly different from those seen in the nonamplified cell lines. In the component planes, the expression patterns are illustrated using a specific color scheme, where shades of red correspond to increase in expression, shades of yellow to stable expression, and shades of blue to decrease in expression during the time series