Fig. 3

Identification of a distinctive eccDNA profile in ALS based on split-reads differential analysis. A For differentiation of PpGCs in ALS and control samples, boundaries were set at log₂ FC 1 (FC 2 in linear scale) as indicated in the pairwise scatter plot by diagonal black lines. PpGCs spectra are visualized by histograms (blue). Those up- or down-produced in abscissa compared with ordinate samples are shown with green and red dots, respectively; orange dots indicate significant DPpGCs from selected genes. Color bar depicts scattering density, with darker blue corresponding to higher scattering density. PpGCs levels are scaled in log₂. B Volcano plot of the PpGCs in ALS versus control samples. The vertical black lines are the boundaries of the log₂ FC 1 thresholds in the eccDNA production levels between the groups. The horizontal black line is the 2-boundary of the p-value in -log₁₀ scale (corresponding to p-value = 0.01 in linear scale) in ALS versus control samples. PpGCs beyond these thresholds were inferred to be significantly distinct from control eccDNAs and denominated as DPpGCs. Their distributions are visualized by histograms. DPpGCs up-produced in ALS samples are indicated with green dots; orange dots indicate the most significant DPpGCs. C Heatmaps of the 225 genes that led to up-DPpGCs formations in ALS relative to control samples. Color bars codify the value of PpGCs in log₂ scale. Higher level of difference corresponds to a redder color. The -log₁₀ (p-value) of the up-DPpGCs and the FC in log₂ scale are presented in a two-column table to the right of the respective heatmaps. These annotations are displayed in descending order of statistical significance. Gene names in red mark the cases with corresponding proteome changes. A-C: C, control samples; A, ALS samples