Fig. 2.
Fig. 2. Relatedness of the gene expression profile of PEL to normal B cells and cell lines with an immunoblastic or plasma cell phenotype. / (A-C) Gene expression data sets generated from PEL, BL (from AIDS patients), and B-CLL cases are compared with the genes differentially expressed between (A) GC CB and memory (M) B cells, (B) LCLs and CBs, and (C) LCLs and MM cell lines, as identified by supervised clustering using Genes@Work.1314 Supervised analysis allows the identification of differentially expressed genes between cell types defined a priori according to a given criterion. The tumor samples are aligned to the right to visualize the expression of the respective genes in the tumor cells. Columns represent individual samples; rows correspond to genes. Color changes within a row indicate expression relative to the average of the sample population. Values are quantified by the scale bar that visualizes the difference in the ζ score (expression difference/standard deviation) relative to the mean. Genes are ranked based on the z score (mean expression difference of the respective gene between phenotype and control group/standard deviation). The relatedness of the PEL samples to the LCLs or CBs (B) and the LCLs or MM (C) is indicated by their proximity to either subgroup on the vertical axis. The gray area marks the 95% confidence region; the bottom and top margins of the gray area each correspond to a P value of .025 (P values decrease with increasing distance from the x-axis). Closed circles represent PEL cases. (D) Matrix showing the expression of genes associated with an immunoblastic phenotype (immunoblast-associated; down-regulation of CD10 and up-regulation of CD23, CD30, CD39, and MUM-1/IRF-4, as defined by Rowe et al1920) or with a plasma cell phenotype (PC-associated; MUM-1/IRF-4, BLIMP-1, CD138/syndecan-1) and the GC-specific BCL-6 and the memory B-cell marker CD27. BL indicates BL cell lines; BL t-I, BL type I lines; BL t-III, BL type III lines; LCL, EBV-transformed lymphoblasts; PEL, primary effusion lymphoma; MM, multiple myeloma cell lines. For description of matrix, see panels A-C.

Relatedness of the gene expression profile of PEL to normal B cells and cell lines with an immunoblastic or plasma cell phenotype.

(A-C) Gene expression data sets generated from PEL, BL (from AIDS patients), and B-CLL cases are compared with the genes differentially expressed between (A) GC CB and memory (M) B cells, (B) LCLs and CBs, and (C) LCLs and MM cell lines, as identified by supervised clustering using Genes@Work.13,14 Supervised analysis allows the identification of differentially expressed genes between cell types defined a priori according to a given criterion. The tumor samples are aligned to the right to visualize the expression of the respective genes in the tumor cells. Columns represent individual samples; rows correspond to genes. Color changes within a row indicate expression relative to the average of the sample population. Values are quantified by the scale bar that visualizes the difference in the ζ score (expression difference/standard deviation) relative to the mean. Genes are ranked based on the z score (mean expression difference of the respective gene between phenotype and control group/standard deviation). The relatedness of the PEL samples to the LCLs or CBs (B) and the LCLs or MM (C) is indicated by their proximity to either subgroup on the vertical axis. The gray area marks the 95% confidence region; the bottom and top margins of the gray area each correspond to a P value of .025 (P values decrease with increasing distance from the x-axis). Closed circles represent PEL cases. (D) Matrix showing the expression of genes associated with an immunoblastic phenotype (immunoblast-associated; down-regulation of CD10 and up-regulation of CD23, CD30, CD39, and MUM-1/IRF-4, as defined by Rowe et al19 20) or with a plasma cell phenotype (PC-associated; MUM-1/IRF-4, BLIMP-1, CD138/syndecan-1) and the GC-specific BCL-6 and the memory B-cell marker CD27. BL indicates BL cell lines; BL t-I, BL type I lines; BL t-III, BL type III lines; LCL, EBV-transformed lymphoblasts; PEL, primary effusion lymphoma; MM, multiple myeloma cell lines. For description of matrix, see panels A-C.

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