Figure 4.

Gene expression changes combined across three cell lines. (A) Change in gene expression 5, 12, 18 and 24 h after PRPF39 knockdown was assessed for each of the 61 target genes, using a mixed effects model that combines all expression data from three cell lines. The X-axis shows fold change relative to a scrambled control, with identical expression having a value of 1. The Y-axis shows the negative log₁₀ of the P-value from the combined model, with P= 0.05 shown with a dashed line. Identification of each gene and the direction of effect are found in Supplementary Material, Table S2. (B) The panel shows that above the time point, the genes significantly (P< 0.05) increased in expression, with the gene closest to the center being the most significant change. Below each time point are the genes significantly (P< 0.05) decreased in expression with the gene, with the most significant decrease being the closest to the center. Genes in bold achieve a P-value <0.05 corrected for the number of genes tested at each time point and those with an asterisk remain significant when corrected for number of genes and time points.