Gene expression analysis of mouse plasmacytomas and B cell lymphomas. 70 RNA samples from murine B-cell malignancies, comprised of 6 different types of mouse plasma cell tumors and 4 different types of mouse B cell lymphomas, were used for global gene expression studies. A. Kinetics of appearance of 6 different subclasses of plasma cell tumors. Time course of appearance of PCTs after ip injection of pristane. IL6PCs arose spontaneously in lymph nodes of IL-6-transgenic mice, without pristane treatment, as the mice aged. See Table 1 for more details. B and C. Unsupervised hierarchical clustering. Using Affymetrix U74A v2 microarrays, 6424 genes were used for clustering of genes and samples after filtering out genes with more than 50% of A (absence) calls. Correlation-based (uncentered) average linkage clustering was performed on log base 2-transformed data previously centered to mean expression values of each gene. Gene expressions above this mean value are colored red; those expressed below are shown in green. The cluster dendrogram shows 2 major sample clusters: a PCT cluster and a B-cell lymphoma cluster. Samples are coded with 11 different colors based on previously assigned groups. Asterisks indicate samples that clustered in an unexpected manner (see text). In the dendrogram, the PCT samples are colored blue-green and the BCL samples are red-orange. In the first color bar, different viral and transgenic contributions to PCT development are distinguished by different colors. In the second color bar, the 4 types of BCLs are color-coded. In the third color bar, mouse PCTs previously characterized for the fine structure of their Myc-activating chromosomal translocations are identified in this dendrogram. PCT samples having the variant chromosomal translocation T(6;15) are shown in deep blue, type I T(12;15) are shown in red/orange, and type II T(12;15) are shown in light blue. PCT samples having complex chromosomal translocations  are shown in purple, and PCT samples having no identifiable chromosomal translocations are shown in pale black. Boxes without color indicate PCTs with unknown karyotypes.