Figure 6.

SOD1 regulates expression of numerous genes in transcriptional phases. (A) A hierarchical clustering analysis of the differentially expressed genes (DEGs) caused by DNA binding of SOD1. After overlapping the genes in control group of ChIP-Seq and the DEGs in SOD1 knockdown group of RNA-Seq, the heat map was preparation by normalized log₁₀(FPKM+1) of the DEGs. (B) A volcano plot of log₂(fold change) vs. the -log₁₀(padj) for the DEGs in (A). (C, E and F) Relative FPKM values of some key genes in SOD1 knockdown and LD100 treated HeLa cells (INA, UNC13A, PTK6 and NRG1 in (C); PBX2 and FGFR4 in (E); TUSC2 and CRTC3 in (F). (D) An enriched KEGG pathway scatterplot of the DEGs in (A) shows the most affected 20 signaling pathways with high statistical significance. (G) A heat map of the genes regulates by SOD1 at transcriptional levels, drawn using normalized log₁₀(FPKM+1) of the genes. (H and K) Genome browser views of the SOD1 binding sites near TSS of all genes in (G) and in (J) (red for the ChIP-Seq under normal conditions; blue for the Input). (I and J) RT-pPCR tests for the SOD1-regulated genes in knockdown HeLa cells (TUSC2, CRTC3, KCNAB2, SPEG, QRFP, MAF1, DNM2, NFIC, PTK6, TNFRSF25 and FGFR4 in (I); INA, UNC13A and NRG1 in (J)). Data are mean of triplicate samples ± SD (*P < 0.05, **P < 0.01, ***P < 0.001; unpaired Student's t test), and all error bars are SD.