Fig. 5: Integration of eCLIP and RNA-seq identifies splicing regulatory patterns.

a, Normalized splicing maps of RBFOX2 and PTBP1 for skipped exons that were excluded (blue) or included (red) upon knockdown, relative to a set of ‘native’ skipped exons (nSEs) for which the inclusion rate was between 0.05 and 0.95 in controls. Lines indicate average eCLIP read density in IP versus input for indicated exon categories. Shaded area indicates 0.5th and 99.5th percentiles observed from 1,000 random samplings of native events. b, Heatmap indicates the difference between nSE-normalized eCLIP read density at skipped exons that were included (left) or excluded (right) upon RBP knockdown for all profiled HNRNP and SR proteins (see Extended Data Fig. 6a for all RBPs). c, Lines indicate the average number of RBPs with eCLIP peaks at skipped (green) versus constitutive (grey) exons and flanking introns. Spliceosome machinery RBPs were excluded from this analysis. d, Heatmap indicates normalized eCLIP signal at RBFOX2 knockdown-excluded exons in HepG2 cells relative to nSEs for RBFOX2 (top) and all other RBPs within the same binding class and cell type (bottom). See Extended Data Fig. 8c for all labels. e, Lines indicate normalized signal tracks for eCLIP replicates of RBFOX2 and QKI in downstream proximal introns. Black line, mean of 37 non-RBFOX2 data sets in the same binding class; grey, 10th to 90th percentiles.