Fig. 3: Genome-wide analysis of SCISSOR.

a Significantly mutated genes (rows) for 452 head and neck squamous cell carcinomas (HNSC) samples (columns). Each gene has two rows: mutations and shape changes. Left, percentages of mutation and shape variants; right, percentage of variants additionally identified by SCISSOR/percentage of total variants from mutation and shape changes. b Top: percentage of mutations identified across genes (n = 14,390; on/off genes excluded). The x axis represents thresholds for filtering out lowly expressed genes with the number of genes included at each threshold. Each threshold indicates each percentile cutoff for both median and median absolute deviation (MAD) of normalized RSEM values across samples. The error envelopes were constructed by bootstrapping samples of size 200 with 500 repeats (5th, 95th percentile). Low: as a negative control for this experiment, we report log10(P-values) from a two-sided Fisher’s exact test using silent mutations as a negative control. P-value of 0.01 marked by a red dashed line. c Some of the novel genes identified are shown using the consistent format with a. d Recurrent abnormal expression changes in 3′ UTR in LSS. The RNA-seq profile, for example (TCGA-BA-A8YP), shows deep deletion in the middle of the 3′ UTR (green background). The detailed view of the 3′ UTR by the Integrative Genomic Viewer (IGV) shows no spliced junction reads. However, read pairs were aligned to each of the split regions indicated by the arrow, suggesting an aberrant splicing event. e Recurrent structural variants for MTAP. For TCGA-CV-A463, the last few exons of MTAP were deleted (blue background) and the remaining exons were connected to other parts of the genome. f Recurrent alternative transcription start (ATS) for FBLN5. The detailed view of FBLN5 exons 7–9 including the intervening introns is illustrated by the IGV for FBLN5 ATS event (top) and FBLN5 wild type (bottom). The ATS event shows the short reads aligning continuously between intron 7 and exon 8. On the other hand, the wild type shows normally spliced junction reads between exons 7 and 8 with no expression in intron 7. Exons 7–9 are expressed at similar levels.