Fig. 2: Screening cancer-related genes directly regulated by transcription factor E2F1.

A Representative GSEA plots showing that upregulated DEGs were enriched in E2F targets (top) and the G2M checkpoint (bottom) in the RB versus retinal samples. B E2F1-3 were validated by qRT-PCR using clinical samples, in line with blue dot (normal tissues) and red dot (RB samples). C Schematic diagram of E2F1 ChIP-seq in Y79 cells. D Knockdown efficiency of E2F1 was evaluated by western blotting. E The diagram of overlapping gene numbers among E2F1 ChIP-seq profiling, RNA-seq profiling of E2F1-KD (down-regulated genes) and RNA-seq profiling of RB (upregulated genes), created with BioRender website. F, G The pathway analysis of cancer-related genes directly regulated by E2F1 (F) and their corresponding upregulated genes (G). H ChIP-seq tracks of four representative genes. I, J Four representative candidate genes showing downregulation by Lentivirus knockdown in Y79 cells were evaluated by qRT-PCR (I) and western blotting (J). GAPDH or beta Actin served as an internal control. K Proliferation rate of Y79 cells without (Scramble and Ctrl) and with gene downregulation (PCNA, APAF1, APEX1, CKS2) were analyzed by a Cell Counting Kit-8 (CCK-8) assay. ***P < 0.001; **P < 0.01; *P < 0.05, by two-tailed t-test.