Fig. 2

Distinct sequence characteristics between DAEs and nDAEs. A Line graph showing the number of protein-coding and lincRNA genes (1, 2, 3, 4, or 5 or more) that each DAE is interacting with, and the number of DAEs per category, for CP (red) and GZ (blue). B As A, but here for nDAEs. C Box plots showing the median ncER percentile (left) [38], GC content score (middle) [39] or phastcons score (right) [39] for DAEs-CP (red) and DAEs-GZ (blue) that interact with 1, 2, 3, 4, or 5 or more protein-coding and lincRNA genes. Boxes are IQR; line is median; and whiskers extend to 1.5 the IQR. * p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001; ns, not significant (wilcox.test). D As C, but here for nDAEs. E Box plots, showing from left to right ncER percentile [38], GC content score [39], phastcons score [39], Orion score [40], and CADD score [41], for all DAEs (light gray) and nDAEs (dark gray), or for those DAEs and nDAEs that are interacting in CP or GZ with protein-coding and lincRNA genes (red) or genes with a known OMIM phenotype (blue). Boxes are IQR; line is median; and whiskers extend to 1.5 the IQR. * p < 0.05; ** p < 0.01; *** p < 0.001; ns, not significant (wilcox.test). F Box plot showing the pLI score [42] of genes interacting with DAEs (light gray) and nDAEs (dark gray) in CP or GZ. Boxes are IQR; line is median; and whiskers extend to 1.5 the IQR. *** p < 0.001; (wilcox.test). G Kernel density plot showing the distribution of loss-of-function tolerance scores for non-coding sequences [43] for all DAEs (light gray), all nDAEs (dark gray), DAEs linked to protein-coding and lincRNA genes in CP (red), DAEs linked to protein-coding and lincRNA genes in GZ (green), nDAEs linked to protein-coding and lincRNA genes in CP (orange), and nDAEs linked to protein-coding and lincRNA genes in GZ (yellow). H Bar chart showing the most enriched transposable elements (TEs) overlapping with from left to right all nDAEs, all DAEs, DAEs interacting with protein-coding and lincRNA genes in CP, and DAEs interacting with protein-coding genes in GZ. Plotted is a ratio between the observed (O) number of TEs over the expected (E). Different classes of TE are indicated with different colors as indicated