Fig. 1

R-loop score from malignant cells related to lung adenocarcinoma (LUAD) progression. A Clinical and molecular characteristics of the 30 LUAD samples obtained from GEO datasets (GSE123904 and GSE131907), and the proportion of cell types in each sample. B Uniform manifold approximation and projection (UMAP) plot of 92,842 cells colored according to cell types or individual patients. C UMAP plot of 27 identified subgroups from malignant cells. D Weighted gene coexpression network analysis (WGCNA) of 1,185 R-loop regulators. A deeper color indicates a stronger interaction. E Interaction plots of 92 R-loop regulators from purple, brown, magenta, and pink modules. F Malignant cells are divided into high- and low-score groups according to the median value of the R-loop scores. The line graph shows the number of malignant cells in each subgroup, and malignant cells with high scores are in orange. G The differences in the R-loop score for malignant cells in various conditions (Wilcoxon rank test). H Gene set variation analysis (GSVA) showing the differences in the enrichment pathways between malignant cells with high R-loop score and those with low R-loop scores (Bayesian t-test). (*p < .05, **p < .01, ***p < .001)