Fig. 2: Pathogenic mutations and inflammation scores. | Nature Cancer

Fig. 2: Pathogenic mutations and inflammation scores.

From: The immunopeptidome landscape associated with T cell infiltration, inflammation and immune editing in lung cancer

Fig. 2

a, Heat map of detected mutations (n = 157 mutations) that were annotated as pathogenic by the FATHMM prediction in COSMIC. Colors represent different patients and every line is a macro-region (n = 51 macro-regions). Mutations in KRAS, TP53 and EGFR are highlighted in red. b, PCA of genes associated with either LUADs or LUSCs confirming the classification of the samples. The list of genes was taken from Reili et al.15 and is provided in Supplementary Table 3 (n = 53 macro-regions). c, Inflammation scores calculated for each macro-region as well as LUAD and LUSC tumors from TCGA using expression levels of the immune-related gene panel as in Danaher et al.17. The different macro-regions (n = 53 macro-regions) of patients with lung cancer were superimposed on the TCGA data (n = 1,011 TCGA patients). d, Inflammation scores for each macro-region. The scatter plot denotes 53 regions of the 8 different patients; the red color denotes the healthy samples and red boxes denote the regions subjected to GeoMx analysis. In patient 02287, the tissue selected for GeoMx was not subjected to bulk RNA-seq and therefore not shown in this panel.

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