Fig. 4
From: Compartment-specific eccDNA patterns reveal senescence associated biomarkers in hUC-MSCs
The genomic function analysis of eccDNA in long term passage of hUC-MSCs. (A) Normalized ratio of eccDNA in different genomic elements. (B) Normalized mapping ratio of eccDNA reads aligned to repeats. (C) The number of genes associated with eccDNA across different genomic regions: Gene2KU, 5’UTR, Exon, Intron, 3’UTR, and Gene2KD. Positive bars (green) indicate enriched regions, while negative bars (brown) represent underrepresented ones. Values on each bar provide a quantitative comparison across these elements. (D) The distribution of genes associated with different genomic regions, including Gene2KU, 5’UTR, Exon, Intron, 3’UTR, and Gene2KD. The x-axis shows the p-value (− log10), and the y-axis represents the adjusted p-value (padj, − log10). Genes with significant expression changes are highlighted, with thresholds set at p-value = 0.01 and padj = 0.01 (marked by blue lines). Points are color-coded based on their genomic region, with labeled genes representing notable candidates within their respective categories. (E) The distribution of recurrent genes on eccDNAs across P1, P6, and P12. Each bar is segmented by sample count within the respective group, with colors representing the different time points (black for P1, brown for P6, and blue for P12). (F) The enriched biological pathways based on the gene set analysis of recurrent presented eccDNAs. Pathways include the regulation of the actin cytoskeleton, Ras signaling, axon guidance, growth hormone synthesis, secretion, and action, T cell receptor signaling, mRNA surveillance, Fc epsilon RI signaling, biosynthesis of nucleotide sugars, and D-amino acid metabolism. The x-axis indicates the count of genes associated with each pathway, showing the relative enrichment across these biological processes.
