Fig. 2: Impact of splicing factors knockdown on gene expression and pre-mRNA splicing in the HepG2 cell line.

A The heat map shows the percent of genes associated with indicated Gene Ontology terms that have changed their expression or splicing in response to splicing factors knockdown in HepG2 cells (percent is indicated by the gradient green color). B The overlap between genes affected by alternative splicing and differentially expressed genes upon knockdown for each splicing factor (p-values are indicated by the gradient blue color). C The overlap between genes with significantly enriched eCLIP signal and genes with significantly altered expression upon knockdown for each splicing factor (p-values are indicated by the gradient blue color). D The overlap between genes with significantly enriched ChIP-seq signal in promoter regions and differentially expressed genes upon knockdown for each splicing factor (p-values are indicated by the gradient blue color). All data were obtained via the analysis of the publicly available datasets from the ENCODE project. Significance was determined by two-sided Fisher’s exact test (p-value < 0.05 and the odd ratio confidence interval should not include 1). The significant enrichment is indicated by an asterisk. “All genes from 6 pathways” include all genes from 6 Gene Ontology (GO) terms: “Cell population proliferation”, “Cell migration”, “DNA repair”, “Cell senescence”, “Cell cycle”. “Other protein-coding genes” means all protein-coding genes not belonging to the above-mentioned GO terms. Detailed information about bioinformatics analysis of these data is provided in the Supplemental Methods.