Extended Data Fig. 3: TRTpred’s validation and results.

a) Y-random permutation tests (black points, n = 100) results in terms of Matthew′s Correlation Coefficient (MCC), AUC and accuracy. The red square corresponds to the best model results demonstrating its validity. b) Heatmap comparing relevant up and down regulated genes from TRTpred’s signature with 5 published CD8⁺ TILs tumor-reactive signatures (Oliveira et al.¹⁴, Hanada et al.¹², Lowery et al.⁸, Zheng et al.¹¹ and van-der-Leune et al.¹⁷). c) Venn diagrams comparing the up (top) and down (bottom) regulated genes from TRTpred signature (red) with the 5 CD8⁺ TILs tumor-reactive signatures from panel B (grey). Underneath the Venn diagrams are the Jaccard indexes and the list of common genes. d) Heatmap of the Jaccard similarity index matrix comparing the 6 CD8⁺ TILs tumor-reactive signatures from panels B and C. The upper and lower triangle of this matrix correspond to the up and down regulated genes, respectively. Grey boxes correspond to missing gene-sets. e) Heatmap of AUC performances of 6 CD8⁺ TILs tumor-reactive predictive signatures (X-axis) applied on 6 datasets (Y-axis) comprising the input data (melanoma, n = 10), the internal benchmarking data (melanoma, n = 4) and data from 4 cohorts: Oliveira et al.¹⁴ (melanoma, n = 4), Hanada et al.¹² (lung, n = 4), Lowery et al.⁸ (n = 1 melanoma, n = 2 breast and n = 12 GI) and Zheng et al.¹¹ (GI, n = 5). The performance of each model on its original data is highlighted.

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