Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling
J. Clin. Invest. Ralf Küppers, et al. 111:529 doi:10.1172/JCI16624 [
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Figure 2Identification of genes differentially expressed between HL lines, LCL, and ABC-type DLCL lines versus BL and GC-type DLCL. The gene expression profiles of four HL, five LCL, and two ABC-type DLCL lines that clustered together in the unsupervised analysis (see Figure
1) were compared with those generated from six BL and six DLCL (non–ABC-type) cell lines by supervised hierarchical clustering using Genes@Work (see Methods). Columns represent individual cell lines, and 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/SD) relative to the mean. Genes are ranked based on the
z-score (mean expression difference of the respective gene between phenotype and control group/SD). The support value for supervised analysis was chosen as
n =
n0 – 1, where
n0 is the number of cells in the given phenotype set, allowing for one unclustered sample per pattern in the phenotype set. The corresponding expression data for BCL-2 and BCL-6 were obtained by relaxing the criteria in the supervised clustering and are therefore shown separately at the bottom. Gene names and cell lines are indicated.
