Venn diagrams of significantly affected genes. (a) Significantly affected genes following PML knockdown by two independent siRNAs (siP1, siP2) compared to control siRNA (siC) in HUVECs without TNFα treatment. The intersection of both circles (i) is considered significantly affected genes by PML knockdown (designated as “siP.U-siC.U”). (b) Comparison between TNFα responsive genes (“siC.T-siC.U”) and TNFα responsive genes when PML was knocked down (“siP.T-siP.U”). (c) Comparison between PML-knockdown responsive genes in the absence of TNFα treatment (i, “siP.U-siC.U” from a) and in the presence of TNFα treatment (“siP.T-siC.T”). (d) Identification of genes interactively regulated by PML knockdown (two siRNAs, siP1 and siP2) and TNFα treatment. The intersection of both circles (ii) is considered significantly affected interaction genes. Untreated samples, “U”; TNFα treated samples, “T”; comparison between two samples, “-”; interaction effects, “∗”. Numbers in the circles, the number of significantly altered genes (>1.5fold,q < 0.05) by the indicated comparison. Numbers in the outer box, the number of unchanged genes; up-regulation, “up” shown in red; down-regulation, “down” shown in green.
Cheng and Kao BMC Genomics 2012 13:453 doi:10.1186/1471-2164-13-453