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. 2000 Mar 14;97(6):2680–2685. doi: 10.1073/pnas.97.6.2680

Figure 3.

Figure 3

Cluster Analysis of LYar and LYas response to radiation reveals mitochondrial and apoptotic gene induction. (A) To categorize the responses of the two cell lines to radiation, Pearson rank cluster analysis was performed on the average difference (AD, calculated by subtracting the mismatch signal from the perfect match signal) values for all 11,000 genes present on the array (1). The AD value for each gene was subtracted from the AD value for that gene in unirradiated LYas cells to cluster the genes with similar changes in expression levels. Each column presents the expression of that gene at the indicated time relative to unirradiated LYas cells. Red indicates increased expression, and green indicates decreased gene expression. Line length in the dendrogram indicates correlation, with shorter lines indicating greater correlation. Three major groups of genes emerged after radiation. Genes that were induced in both cell lines (red), genes preferentially elevated in LYar cells [fatty acid binding proteins (FABPs), CD53, and fructose-1,6-bisphosphatase] (blue), and genes elevated in LYas cells (see below) (yellow). The complete data set can be found at http://apoptosis.stanford.edu. (B) Radiation-induced genes expressed in LYas and LYar cells. Discrete cluster subsets from above data detailing genes induced by radiation only in LYas cells (Upper) and in both cell lines (Lower). Of the genes induced in LYas cells only, some have previously been implicated in regulating apoptosis (blue), and a subset of mitochondrial genes is also identified (green). Most of the genes induced in both cell lines are ribosomal genes. (C) AD time course for voltage-dependent anion channel (VDAC) and mitochondrial uncoupling protein (UCP) family members from mRNA collected at 0, 15, 30, 45, 60, and 120 min after 5 Gy of irradiation. Significant mRNA message increased only for UCP-2 in the LYas cells (Left). VDAC-1 is the only family member that increased dramatically (Right). Increased message is detected immediately after radiation exposure and plateaus at 1 hr.