Genes showing differential expression between myeloma and nonmyeloma cell lines.

Two-class SAM11 analysis was used to identify the genes differentially expressed in the myeloma and nonmyeloma cell lines. Using a false discovery rate of 0.5%, 94 genes were selected. Those genes showing statistically significant differences between the 2 groups are shown as a cluster image. (A) Two-dimensional heat map view. The dendrogram (top) indicates nonmyeloma hematopoietic cell lines (5 lymphoma and 1 leukemia) in red and myeloma cell lines in green. The myeloma cell lines cluster together, as do the nonmyeloma cell lines. The bar on the left of the 2-dimensional heat map indicates down-regulated genes in myeloma in green and up-regulated in red. The color at each position indicates the level of gene expression for a single cDNA in a cell line, with red indicating high expression and green indicating low expression. (B) Three-dimensional landscape view of cluster results. This view adds the level of gene expression as an additional dimension to the 2-dimensional view. The roughness on the landscape indicated the level of variability. Myeloma cell lines are on the right of the yellow axis bar, and nonmyeloma lies on the left. (C) The SAM analysis data, which generated 279 cDNAs that are up- or down-regulated between the 2 groups of cell lines, are illustrated graphically with δ = 1.4 and a false-positive rate of 0.5%. After immunoglobulin genes and duplicate cDNAs were removed, 94 genes were used to produce the heat map shown in panel A. Of the 94 genes, 52 were ranked based on the SAM result as shown in Table 3. (D) RT-PCR analysis of selected genes confirmed differential expression of representative differentially expressed genes shown in panel A.