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. 2019 Oct 17;17(2):227–239. doi: 10.1080/15476286.2019.1674595

Figure 2.

Figure 2.

Comparison of differentially expressed genes in eRF3A and UPF1 knockdown cells. (A and B) Proportional Venn diagrams showing the overlap of differentially expressed genes (adjusted p‐value, p adj < 0.05, DESeq2) between eRF3A knockdown and UPF1 knockdown targets for RNA-seq (A) and Ribo-seq (B) data. For each Venn diagram, the number of differentially expressed genes are indicated. (C) Scatter plot comparing Ribo-seq (y axis) and RNA-seq (x axis) log2 Fold Change (log2FC) for eRF3A-depleted versus control cells (eRF3A KD). Green circles indicate genes with p adj < 0.05, dotted purple lines indicate 1.5 fold change (log2FC = ± 0.585). (D) Enlargement of the dotted rectangle in C. Some transcriptional regulator genes are indicated by red dots. (E) Scatter plot comparing Ribo-seq (y axis) and RNA-seq (x axis) log2 Fold Change (log2FC) for UPF1-depleted versus control cells (UPF1 KD). Green circles indicate genes with p adj < 0.05, dotted purple lines indicate 1.5 fold change. Some transcriptional regulator genes are indicated by red dots. (F) Expression heatmap of a selection of transcriptional regulators for eRF3A and UPF1 knockdown cells. Heatmap was performed using Heatmapper website http://www2.heatmapper.ca/expression/[85] and Complete Linkage clustering method.