Extended Data Fig. 7: Characteristics of PC phenotypes.
a. Boxplot showing the proportions of SMCs and PCs in ANT (n = 77) and tumour (n = 265) samples, respectively. b. Violin plot showing cell purity for SMC (n = 10,819) and PC (n = 29,572) by ROGUE. Error bar represents mean ± standard deviation. c. Bar plot showing the cell number (top) and percentages (bottom) of cancer types across MC subtypes. Box plot showing the mean proportions of each cancer type between ANT (n = 77) and tumour (n = 265) samples across MC subtypes. d. UMAP plot showing the density of quiescent score. MatPCs showing heterogeneous quiescent states. e. Heatmap showing the activities of energy metabolism pathways among PC subclusters. f. Boxplot showing cell purity of MC subtypes by ROGUE. SMC, n = 10,819, adiPC, n = 2,562, matPC, n = 10,230, myoPC, n = 5,599, vdPC, n = 11,181. g. Visualization of the matPC trajectories inferred by Slingshot, VIA, and Monocle3. h. Boxplot showing the CytoTRACE score among matPC subtypes. BASP1+ matPC, n = 2,060, inter. matPC, n = 4,211, matPCQ, n = 3,959. i. Loess regression-smoothened gene expression of the oxidative-stress genes (y-axis) associated with in pseudotime. Violin plot showing the expression levels of corresponding genes. j. Violin plot showing the SCENIC scores of ATF3 (right) and XBP1 (left). BASP1+ matPC, n = 2,060, inter. matPC, n = 4,211, matPCQ, n = 3,959. k-l. Loess regression-smoothened expression (y-axis in k) and SCENIC activity (y-axis in f) in pseudotime. Spearman’s correlation coefficient and its P-value are shown in f. ****, P < 0.0001. m. TF activity in BASP1+ matPC. ER-stress-related TFs were labelled. Shaded region represents the 95% confidence intervals (i, k, and l). For boxplots, centre line represents median, box limits indicate upper and lower quartiles, and whiskers extend 1.5 times the interquartile range. Statistical analysis was performed using two-sided Mann–Whitney U test (a, b, and c) and Kruskal–Wallis test (f, h, and j).
