Fig. 3: The features of ncORFs with high PepScores.

a The PepScore distribution of human ncORFs. b Number of ncORF types with PepScore > 0.6. These high-PepScore ORFs were used in the following panels (c–i). c The length distribution of ncORFs. The boxes are bounded by the 25 and 75 percentiles and the center represents the median. The whiskers extend from each edge of the box to indicate the 1.5x interquartile range. The numbers of ncORFs used in the plot are shown in (b). d The PhyloCSF score of ncORFs. The boxplot format is the same as described in (c), and the numbers of ncORFs are shown in (b). e Fraction of high-PepScore ncORFs with a protein domain. f Fraction of the ncORFs conserved in different species. g Fraction of the ncORFs conserved in mouse, grouped by ORF types. h The Tau index measuring the tissue-specific expression of the indicated ORF types. The boxplot format is the same as described in (c). The numbers of ncORFs are shown in (b), and 33,238 canonical ORFs were analyzed for the comparison. i The DeepLoc-predicted peptide localization, grouped by ORF type. j The distribution of PepScores for the peptides detected by mass spectrometry, including 326 peptides detected in the whole proteome and 1480 bound by MHC I. The P-value calculated using the two-sided Wilcoxon Rank Sum Test is shown. k The distribution of phenotype scores after CRISPR knockout of the ORFs in iPSCs. The ORFs were grouped by PepScore: 60 ncORFs with high PepScores (>0.6) and 854 ncORFs with low PepScores (≤0.6). The P-value calculated using the two-sided Wilcoxon Rank Sum Test is shown.