Figure 1

Schematic diagram of microarray data analysis. HeLa^{TetO-FLAG-IκBα Mut} cells were plated in parallel into cultures in the absence or presence of Dox (2 μg/ml). After four days, cells were stimulated without (0 h) or with rhTNFα (25 ng/ml) at 6 h, 3 h, and 1 h prior to simultaneous harvest for RNA extraction. Experiments were conducted four independent times. Data sets were scaled for comparison. NF-κB dependent genes were identified using 2-way ANOVA where Dox treatment and TNF treatment were considered independent variables. Those changed by Dox treatment at a p-values [Pr(F)< 0.01] were then filtered for 3-fold change at any point during the experiment (signal intensity with NF-κB vs signal intensity without NF-κB).