Fig. 2

Gene expression comparisons in TcA cells exposed to dsmalE or dsCBP and treated with JH III and TSA using the empirical analysis of DGE (EDGE) algorithm in CLC Genomics Workbench (Version: 9.5.9). (a-e) Heatmaps showing the overall comparison between DMSO and JH III treated cells exposed to dsmalE (MD vs. MJ), DMSO treated cells exposed to dsmalE or dsCBP(MC vs. CD), DMSO or JH III treated cells exposed to dsmalE or dsCBP(MD vs. CJ), DMSO or TSA treated cells exposed to dsmalE or dsCBP (MD vs CT), and DMSO or TSA treated cells exposed to dsmalE (MD vs. MT) (Table 1). The dsmalE plus DMSO treated cells act as a control. The color spectrum, stretching from yellow to blue, represents TMM (trimmed mean of M values) normalized expression values obtained after EDGE analysis. (f-j) Volcano plots of expression data after EDGE analysis. The red dots indicate the number of significantly up- and down-regulated genes using p < 0.01 and ± 2-fold change as the cut-off threshold corresponding to each comparison