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. 2024 Nov 14;15:9886. doi: 10.1038/s41467-024-54182-5

Fig. 2. Genes that validate both in TCGA test sets and in external cancer cohorts.

Fig. 2

a Violin plots show the distribution of the Pearson correlation coefficient (left y axis) of genes that validate both CPTAC and TCGA test set. Within each violin plot, a miniature box-and-whisker plot is shown where whiskers bound the min–max values of the data, the bounds of the box represent lower (Q1)/upper (Q3) quartiles, and the central value contains the median value. The top 1000 genes with the highest correlation coefficients obtained from each model are shown. Black squares indicate the absolute number (right y axis) of genes that validate both TCGA test set and CPTAC. b Same as (a) for Normalized RMSE. Note that mlp_res did not have any significant genes that overlap between TCGA-CPTAC for LUSC, PAAD, KIRC (Supplementary Table 9) and hence violin plots for these settings do not exist. Source data are provided in the Source Data File.