Extended Data Fig. 7: RNA-seq analysis reveals 471 DEGs in CUX1 siRNA-treated human ECs.
From: Post-GWAS functional analysis identifies CUX1 as a regulator of p16INK4a and cellular senescence
A. Heatmap showing the top 20 upregulated and downregulated DEGs including DDAH1 and DNMT3b 48 hrs after CUX1 was knockdown by siRNA. Gene expression is shown in normalized log2 counts per million. DEGs were selected based on a more than 1.5 FC between CUX1 siRNA-treated samples versus scrambled siRNA-treated samples and adjusted P-value less than 0.05. CUX1 and p16INK4a, p14ARF, and p15INK4b are among the top 20 downregulated DEGs. B. Volcano plot showing 471 DEGs with the log2FC in the CUX1 siRNA-treated human ECs. The x-axis displays logFC between CUX1 siRNA-treated samples versus scrambled siRNA-treated samples(logFC.E2D) and the y-axis displays −log10 adjusted P-value. Genes with log2FC outside the range −2 to +2 were squished to this range. DEG2 in blue including CDKN2A, TNFRSF10B, CXCL1, CXCL12 and CCL2 were previously identified as endothelial senescence-related genes67. The top 5 upregulated and downregulated DEGs were also listed, they are CDKN2A, CUX1, DDAH1, GNAT1, CDKN2B, RP11-301G19.1, MET, MX1, IFI44L, NRK. C. List of the 29 upregulated and 5 downregulated pathways with NOM p-value < 0.05 in the CUX1 siRNA-treated human ECs.
