Figure 2. Rational Combination of Neoantigen Predictions Improve Prediction Performance.
(A) Overview of each pMHC across all of TESLA that validated in a multimer-based assay. For each pMHC, the rank of that pMHC for a given team is shown. Places where a team did not identify a particular pMHC in any of their submissions are shown in gray. Bottom: for each peptide, the fraction of time that peptide was ranked in different ranking groups (left).
(B) Schematic of prediction combination method along with metric calculation.
(C) Histogram of average change in combined TTIF. Yellow, combination improves prediction on average; blue, combination is detrimental to prediction on average.
(D) Density plot of average overlap, stratified by improvement status. Distributional difference assessed by Kolmogorov-Smirnov test.
(E) Boxplot of relative difference stratified by improvement status. *p < 0.05.
(F) Scatterplot of average overlap by relative difference. Ellipses represent best fit at one standard deviation. Rho, Spearman rho.
(G) Combined TTIF by the average of the two initial TTIF values, by team pair and patient. Color represented improvement status (as in C), and shape represents if a particular value was a global improvement (larger than all previous TTIF values for that patient, triangle) or not (circle). (F) Fraction of predictions that are global improvements stratified by whether average team-pair TTIF is above or below the median. *p < 0.05.