Fig. 1

Intersection of SVs with SEs in non-CAGAs LUAD. A Bioinformatics methodology employed to detect SEs that are potentially regulated by SV events. Given the extensive perturbations to the 3D genomic architecture associated with SV events, a significant association is inferred when a 20-kb region surrounding the genomic breakpoint exhibits a substantial overlap with an SE region. A comprehensive description of the methods can be found in the method section. B Comparison of log₂ frequency of SV events per sample (left side) and SE-SV overlaps per sample (right side) between CAGAs LUAD (n = 45) and non-CAGAs LUAD (n = 174). Statistical analysis was conducted using a two-sided t-test. * P < 0.05, ns: not significant. C KEGG pathway enrichment analysis on gene clusters annotated as SE regions with concurrent SVs in non-CAGAs LUAD samples. The statistical significance of the enriched pathways was determined using the enrichKEGG function from the clusterProfiler R package. The background gene set was defined as genes annotated with the SV regions alone. Comparable results were observed when using genes annotated with SE regions alone as the background (data not shown). False discovery rate (FDR) was calculated using the Bonferroni correction method, and the q-scores (qscore) were represented as -log₁₀(FDR). The 20 enriched pathways are displayed (FDR < 0.05). D The gene clusters obtained from the top 5 enriched pathways in non-CAGAs LUAD. The counts of individual genes annotated in regions where SE and SV overlaps were provided