Differentially expressed genes in AHI-1–suppressed cells identified through microarray analysis. (A) Venn diagram of differentially expressed probes selected by both Limma and dChip analyses. The Affymetrix GeneChip Human Genome U133 Plus 2.0 Array screened 54 330 probe sets using the threshold values of a fold change of 2 or higher and 2 or lower and a P value of .01 or less for differential expression. Initial Limma analysis selected 283 differentially expressed probe sets, which was further refined to 33 with the BH P value adjustment. Importantly, the 119 probes sets identified by dChip analysis completely overlapped the initial Limma results. (B) Volcano plot of differentially expressed probes selected by Limma analysis (red represents up-regulated; green, down-regulated; and +, after BH adjustment). (C) Heat map of differentially expressed genes from the refined Limma (BH) analysis. Up-regulated (red) and down-regulated (blue) genes are defined by comparing the pooled gene expression of Hut 78/sh4 bulk and Hut 78/sh4 clone 1 samples with Hut 78 and Hut 78 RPG samples.