Two-dimensional hierarchical cluster analysis of experimental expression profiles and gene behavior.
(A) Cluster-ordered data table. The clustering is presented graphically as a colored image. Along the vertical axis, the analyzed genes are arranged as ordered by the clustering algorithm. The genes with the most similar patterns of expression are placed adjacent to each other. Likewise, along the horizontal axis, experimental samples are arranged; those with the most similar patterns of expression across all genes are placed adjacent to each other. Both sample and gene groupings can be further described by following the solid lines (branches) that connect the individual components with the larger groups. The color of each cell in the tabular image represents the expression level of each gene, with red representing an expression greater than the mean, green representing an expression less than the mean, and the deeper color intensity representing a greater magnitude of deviation from the mean. (B) Amplified gene cluster showing genes down-regulated in MM. Most of the characterized and sequence-verified cDNA-encoded genes are known to be immunoglobulins. (C) Cluster enriched with genes whose expression level was correlated with tumorigenesis, cell cycle, and proliferation rate. Many of these genes were also statistically significantly up-regulated in MM (χ2 and WRS test) (Table 5). (D) Dendrogram of hierarchical cluster; 74 cases of newly diagnosed untreated MM, 5 MGUS, 8 MM cell lines, and 31 normal bone marrow PC samples clustered based on the correlation of 5483 genes (probe sets). Different-colored branches represent normal PC (green), MGUS (blue arrow), MM (tan), and MM cell lines (brown arrow). (E) Dendrogram of a hierarchical cluster analysis of 74 cases of newly diagnosed untreated MM alone (clustergram not shown). Two major branches contained 2 distinct cluster groups. The subgroups under the right branch, designated MM1 (light blue) and MM2 (blue) were more related to the MGUS cases in Figure 1D. The 2 subgroups under the left branch, designated MM3 (violet) and MM4 (red) represent samples that were more related to the MM cell lines in Figure 1D.
