Cyclin T1 specifically affects genes regulated by PMA. (A) For probe sets that were induced >2-fold by PMA treatment, fold-change for shRNA-T1 versus shRNA-Con treatment was calculated. Based on magnitude of the fold-change, a total of 26 categories (bins) were created. The first bin included all the probe sets with a fold-change < -8 and the last bin included all the probe sets with a fold-change >8. For bins between -8- and 8- fold (-3 to 3 after log2 transformation), the probe sets were divided into 24 bins with a log2 transformed value of 0.25 as the range for each bin (-3 to -2.75, -2.75 to -2.5, etc.). The number of probe sets in each bin (frequency) was tabulated and is shown on the Y axis. A histogram was generated based on the frequencies in each corresponding bin, representing the distribution of the fold-changes for those probe sets. The black solid line represents the histogram generated from microarray data from non-PMA-treated cells, while the red broken line represents the histogram generated from the microarray data from PMA-treated cells. (B) For the probe sets that were repressed >2-fold by PMA treatment, fold-change for shRNA-T1 versus shRNA-Con treatment in non-PMA-treated or PMA-treated cells was calculated. A histogram was generated as described above based on the distribution of the fold-changes of those probe sets. (C) Genes that were either upregulated or downregulated by cyclin T1 knock-down were divided into three classes: PMA-induced genes (PMA-Up), PMA-insensitive genes, and PMA-repressed genes (PMA-Down). Number of genes in each category was calculated from the microarray data. Those numbers were then divided by the total numbers for the PMA-induced genes, PMA-repressed genes, or PMA-insensitive genes to obtain the corresponding percentage.