Method of analysis. (A) The difference in mode expression between exons in two biological groups (ER+ HER2−, ER− HER2−, HER2+, and NBS) was computed as the log2 FC for each exon of a gene and the distribution (density plot) of log2 FC for all exons in each gene was plotted. The density plots shown for TP53BP1, TPD52, and IQCG compares one selection of 60% of ER+ HER2− samples to one 60% selection of ER− HER2− samples, and was repeated 100 times for each pairwise comparison. The highest peak represents an overall scaling effect, affecting the majority of exons. Genes not affected by differential splicing will have only one peak, as shown for TP53BP1. The remaining exons, i.e. those in peaks with smaller amplitude, were identified as exons that are differentially spliced or transcribed. Peaks to the right (IQCG) indicate exons with greater log2 FC compared to the exons in the central peak. Peaks to the left of the central peak (TPD52) are exons with smaller log2 FC than the exons in the central peak. Log2 FC was calculated for random selections of 60% of all samples within a biological class 100 times. For each test an exon was called either +1, −1, or 0, so that each exon was tested 10.000 times, and the total score for each exon was determined. The total scores for each exon in the three genes, TP53BP1, IQCG, and TPD52 when comparing ER− Her2− and ER+ HER2− samples are shown in (B). Exons with scores exceeding 3 standard deviations (blue line) were called in the final analysis.