Fig. 3: Genomic and RNA features associated with JTE-607-induced gene expression changes.

a Top features correlated with gene expression regulation by JTE-607 (10 μM) in HepG2 cells. Features are sorted by their individual R² values, with blue color indicating negative correlation with gene expression changes and red color positive correlation. Cumulative R² of a feature (shown in gray) is based on the feature combined with all other features that have a higher individual R². b Schematic showing calculation of the RNA stability score, which is the ratio (log₂) of RNA abundance of pre-existing RNA (FT) to newly made RNA (4sU labeled). c Boxplots showing that GC content is correlated with gene size, gene density, or RNA stability score. All genes with detectable expression (n = 11,663) were divided into five equally sized bins based on the GC content of genic region. The top and bottom of each box represent the 75th and 25th percentile values, respectively; the median is shown as a line in the box. d Bar graph showing overall R² after removal of either GC content or RNA stability score feature, or both. e Scatter plot showing correlation of gene expression changes (log₂Ratio) between HeLa cells (left) or HepG2 cells (right) treated with 10 μM JTE-607 (this study) and HeLa cells with PCF11 siRNA knockdown (a previous study by Kamieniarz-Gdula et al.). Genes with detectable expression in all samples (n = 8584) were used. Pearson correlation coefficient (r) is indicated in each plot. Source data are provided as a Source Data file.