ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer
Fig 3
Splicing epitopes in ten breast cancer cell lines.
(A) For each breast cancer cell line analyzed, the bar plots show the number of splicing alterations measured and the number of cases leading to a change in the reference protein. Alterations shown are alternative 5’ or 3’ splice-site (A5_A3), de novo exonizations (exonization), intron retentions (IR), and new exon skipping events (neoskipping). (B) Number of splicing-derived neoepitopes (splicing-neoepitopes) (red) and splicing-affected self-epitopes (self-epitopes) (blue) for each of the splicing alterations in each of the breast cancer cell lines tested. (C) as in (C) but separated by HLA-type. (D) Example of a splicing-derived neoepitope from a neoskipping event in the gene SIL1 validated with MHC-I associated mass spectrometry in the cell line BT549.