Fig. 6: Contribution of ecDNAs to the cellular transcriptomic heterogeneity.
From: Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines
a The number of ecDNA in different cell lines and ecDNA amplicons with oncogenes accumulate in cells. A one-tailed hypergeometric test was used to test the statistical significance. b ecDNAs with oncogenes (n = 2149), compared to ecDNAs with non-oncogenes (n = 5469), appeared in a higher proportion of cells within individual cell line. For each boxplot, the center line represents the median, the box indicates the upper and lower quartiles and the whisker represents 1.5-fold of the interquartile range. Each dot stands for the cell proportion of cells with one specific ecDNA within an individual cell line. A two-sided Wilcoxon test was used to test the statistical significance. c The correlation between the relative coverage number of ecDNAs and the RNA expression level of genes that appeared in ecDNAs. Spearman’s rank correlation coefficient was used to evaluate the correlation between the scATAC-seq read coverage of ecDNA amplicon (x-axis) and the RNA expression level. A two-tailed Spearman correlation test was used to test statistical significance. d The expression of genes appearing in ecDNA regions in the subcluster of SCC-4. e The percentage of ecDNA-positive cells and high expression cells was correlated in SCC-4. f UMAP map of coverage of ecDNA (chr12: 5900000_7200000). Each dot represents a cell, the color from blue to yellow represents the coverage from low to high, and the red circle marked out is cluster 0 of MDA-MB-231 (n = 208 in cluster 0, n = 687 in cluster 1, and n = 724 in cluster2). For each boxplot, the center line represents the median, the box indicates the upper and lower quartiles and the whisker represents 1.5-fold of the interquartile range. A two-sided Wilcoxon test was used to test the statistical significance. g The expression of genes located on ecDNA (chr12: 5900000_7200000) in different clusters (n = 208 in cluster 0, n = 687 in cluster 1, and n = 724 in cluster2). For each boxplot, the center line represents the median, the box indicates the upper and lower quartiles and the whisker represents 1.5-fold of the interquartile range. A two-sided Wilcoxon test was used to test the statistical significance. Source data are provided in the Source Data file.
