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. 2023 Nov 28;14:7805. doi: 10.1038/s41467-023-43651-y

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a Boxplot of $p_{s v - g e n e}^{p h e n}$ scores (y-axis, $α = 1$ ) in four groups of driver genes affected by 91 coding SVs predicted by the original study on congenital abnormality (x-axis). Median (center line), IQR (box limits), and outliers (points) that exceeding 1.5x IQR were shown in the boxplot. b Displayed are input × gradient values of top 50 important features (row) for each genome segment (column) of the SV (chr16:28473235-30186830, deletion, GRCh38), including protein-coding genes segments (black borders) and intergenic noncoding segments (no borders). Colors of column names represent values of $p_{s v - g e n e}^{p h e n}$ ranging from 0 (blue) to 1 (red) with $α = 1$ . c Transmission rate of paternal (case: n = 100, control: n = 26, left panel) and maternal (case: n = 79, control: n = 17, right panel) noncoding SVs to cases and controls with (blue and red) and without (black) being stratified by $p_{s v - g e n e}$ . Error bars represent 95% CI of transmission rate, where the center is observed transmission rate. d Displayed are cumulative affected sample numbers (y-axis) with $p_{s v}$ (left panel), $p_{s v - g e n e}$ of the most affected epilepsy gene (middle panel), and $p_{s v - g e n e}$ of the nearest epilepsy gene (right panel) larger than given thresholds (x-axis) of 150 patients and 150 controls on average. Confidence intervals of controls (blue shade area between dashed lines) are calculated by randomly sampling 150 samples from 223 controls for 100 times. Area of orange shades represent enrichment score, defined as integrated cumulative number of affected patient samples over upper bound of the 95% confidence interval of controls. e–g Displayed are input × gradient values of top 50 important features (row) for each genome segment of the SVs affecting SOX9 gene (e: Gordon et al.⁵⁹, GRCh38, chr17:70685120-70964563, deletion; f: Kurth et al.⁶⁰, GRCh38, chr17:70134929-71339950, duplication; g: Benko et al.⁶¹, GRCh38, chr17:71072938-71767918, duplication). Genome segments (column) include SV segments (red borders) and distal genes within TAD (no borders). Colors of column names represent values of $p_{s v - g e n e}$ ranging from 0 (blue) to 1 (red). Source data are provided as a Source Data file.