Fig. 5

Tumor-specific isoforms and neoantigen candidates in clinical samples. a The number of splicing isoforms and the proportion of each splicing event (upper panel), and genes included in the NMD complex (lower panel) for each specimen. Cases 3 and 4 show more isoforms and harbor damaging mutations in NMD factors. b A comparison between the isoform expressions of non-tumor and tumor tissues in case 2. Red points represent tumor-specific isoforms (TPM in tumor tissue ≥ 10 and a fold change of TPM ≥ 2). The green area shows isoforms with 0 TPM in normal tissue and the blue area shows fold change of TPM ≥ 2 isoforms. c Correlation between the number of isoforms and the TMB for each specimen. No significant correlation was observed (r = − 0.46). d The full-length structure of splicing isoforms of SMOC2 in case 3. Unannotated exons were detected between exon 7 and exon 8. e The number of neoantigen candidates in each specimen. f The distribution of the maximum NetMHC score for each isoform or mutation type. *P < 0.05 (Kruskal–Wallis test and Dunn–Bonferroni’s post hoc test)