Gastric Cancer Cell Lines Have Different MYC-Regulated Expression Patterns but Share a Common Core of Altered Genes

Figure 5

Common DEGs enriched in three GC cell lines after MYC-silencing. (a) Using Venn diagram, we were able to identify 14 common DEGs among AGP01, ACP02, and ACP03, but each one of them also has a unique set of DEGs. (b) Identification of the 14 common DEGs in 8 enriched hallmarks of collection H, represented by the % of its correspondent ES, ES scores are shown inside the pie chart for each hallmark. (c). Heatmap for the expression of the 14 common DEGs shared for three GC cell lines after MYC-silencing. Blue represents downregulation while red means upregulation. Notice that, even for the 14 common genes, each cell line has a different expression pattern. Relative read expression was normalized using log₂ Fold-change between MYC-silenced/control siRNA. (d) Heatmap for the relative gene expression obtained by RT-qPCR for the 14 identified DEGS for the AGP01, ACP02, and ACP03 cell lines. (e) The overall expression for the 14 DEGs is downregulated in the ACP02 cell line when compared to AGP01 cells. (f) The gene expression levels were increased in ACP03 cell line, but no statistical difference was found. (g) Relative gene expression was increased for ACP03 when compared to ACP02. Wilcoxon matched-pairs signed rank test was used to compare the relative gene expression levels (^∗P <0.05, ns: not significant, and ^∗∗∗P <0.0001).

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