Global gene expression changes associated with RNAi. (A) Summary of gene expression data. Global gene expression patterns in three siRNA experiments were analyzed; in each set the gene expression of cells which were mock transfected (no siRNA), transfected with GFP siRNA, or cognate control siRNA were determined in parallel in triplicate. Data sets: (E1) HEK293 cells with transiently expressed GFP target treated with E1, C1, or no siRNA; (E2) HEK293 cells with transiently expressed GFP target treated with E2, C2, or no siRNA; (stable) Phoenix cells stably expressing an integrated GFP gene treated with E1, C1, or no siRNA. Genes that had signal intensity >1.5-fold of the local spot element background in the reference channel and were present for >80% of the data set were considered well measured. The number of well measured genes are shown on the second column; these genes were analyzed in the multiclass comparison by using SAM (15). The number of genes that had an estimated FDR of <0.05 and the FDR of the top 10 performing genes for each data set are shown on the right two columns. (B) Minimal gene expression changes associated with siRNA-mediated RNAi. The 10 genes with the most consistent changes in expression in response to the experimental manipulation, in each of the three siRNA experiments, were collated into a nonredundant gene list. The expression changes of this group of genes in all experiments are displayed in matrix format (16). The expression ratios was mean-centered within each data set, and the gene expression changes are indicated by the color scale as indicated below.

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