Fig. 2: SCISSOR results at the gene TP53.

a Global outlyingness scores and local outlyingness scores are shown in the top and bottom figures, respectively, with kernel density estimates. The colored points indicate the identified shape changes from each step based on the cutoff values (significance level = 1e−04) indicated by the black vertical lines. Each procedure identified 26 global shape changes (GSCs) and 24 local shape changes (LSCs). b Association between mutations and shape changes are summarized. The numbers of coincidences of each mutation and identified GSCs and LSCs are shown in the pie charts (n = 452). c Coverage of a sample with a normal splicing pattern in spite of a splice site mutation is shown (black curve) with median coverage (gray curve). d The reads aligned to the exon-intron junction involved in the splice site mutation are all normally spliced and a subset of those reads are shown using the Integrative Genomic Viewer (IGV). e The ratio of normally spliced reads to reads aligned to the last base of the exon is shown for all samples (n = 452; gray for nonoutliers; red for GSCs; blue for LSCs) using a box plot with the median, interquartile range (IQR), and 1.5×IQR distances from the upper and lower ends of the box marked. The particular sample (black point) has a large ratio close to 1, indicating normal splicing. f Coverage of one of the identified shape changes in the absence of any mutation is shown (black). g A subset of the aligned reads to the region of intron retention is shown using the IGV, which appears as an insertion (T) at 7,579,308–7,579,309 in all the reads abnormally retained. h The ratios of normally spliced reads at this region are shown using a box plot with the median, interquartile range (IQR), and 1.5×IQR distances from the upper and lower ends of the box marked (n = 452; gray for nonoutliers; red for GSCs; blue for LSCs). The box plot shows that the sample (TCGA-BA-6871-01A) and a few other samples identified by SCISSOR have a large proportion of abnormal reads.