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Fig. 3 | Journal for ImmunoTherapy of Cancer

Fig. 3

From: Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment

Fig. 3

MS-detected and predicted neoantigens in five PDOs. a log2 gene expression of all genes harboring a mutation that encodes for an amino acid alteration. The three genes from which neoantigens were identified by MS are highlighted in red. b Number of mutations that encode for amino acid changes (missense, frame-shift and stop-loss mutations), genes predicted to generate strong binders predicted by NetMHCpan4.0 (defined as percentile rank below 0.5%), and strong binder-generating genes that are expressed, compared to MS-detected neoantigens. c HLA percentile rank from NetMHCpan4.0 for all predicted strong and weak HLA-binding neoantigen peptides in the two PDOs harboring MS-detected neoantigens. Predicted neoantigens were ordered from lowest to highest rank, with the predicted ranks of MS-detected neoantigens highlighted in red

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