Fig. 2: Classification of malignant and non-malignant epithelial cells and their heterogeneity and consistency.

a UMAP plot showing the malignant minus non-malignant scores of epithelial cells. b UMAP plot showing the distribution of malignant and non-malignant epithelial cells. Purple indicates malignant epithelium, while green indicates non-malignant epithelium. c Stacked histogram showing the relative percentages of malignant and non-malignant epithelial cells among the total epithelial cells in different sample types. d UMAP plots showing the density of epithelial cells in different sample types. e Scatterplot showing the differentially expressed genes (DEGs) between primary malignant and non-malignant cells. The X-axis indicates the log₂ (mean+1) in primary non-malignant cells, while the Y-axis indicates the log₂ (mean+1) in primary malignant cells. f Scatterplot showing the DEGs between primary and metastatic malignant cells. The X-axis indicates the log₂ (mean+1) in metastatic malignant cells, while the Y-axis indicates the log₂ (mean+1) in primary malignant cells. g Volcano plot showing the DEGs between primary and OM malignant cells. h Bar graphs showing the significantly enriched pathways of genes highly expressed in OM malignant cells. Hypergeometric test; P < 0.01. i Heatmap showing hierarchical clustering based on the number of genes shared by two programs derived from NMF analysis. Each dot represents one program from an individual sample. Seven highly correlated meta-programs were identified. *two programs share more than 20 genes. j Violin and box plots showing the scores of seven meta-programs in malignant cells from PT, OM, PM, and AS (n = 29,592 cells). The center line of the box represents the median value, the upper and lower limits of the box represent the 25th and 75th percentile points. In e–g and j, Wilcoxon rank sum test followed by Bonferroni’s multiple-comparison test. In c, i and j, AD adjacent normal gastric tissues, PT primary gastric tumors, OM ovarian metastases, PM peritoneal metastases, AS ascites samples.