Extended Data Fig. 2: Analysis of cell types and definition of subtypes, related to Fig. 1.

a, Kaplan-Meier plots illustrating the overall survival (OS) of patients grouped by cell percentages across cell types. The log-rank test was used. b, R_o/e indicating tissue site preference of cell types in gallbladder adenocarcinoma patients. c, Boxplots showing tissue site preference of B, dendritic, mast, and mesenchymal cells. n for Pri, PO, LN, LI, LM, and OM groups are 75, 1, 11, 10, 5, and 2. The Benjamini-Hochberg-adjusted two-sided Wilcoxon test was used. d, Boxplots showing sex preference of plasma and dendritic cells. n for male and female groups are 24 and 51. The two-sided Wilcoxon test was used. e-i, UMAP plots showing the expression of canonical marker genes of cell subtypes, including CD8⁺ T cell subtypes (e), CD4⁺ T cell subtypes (f), DC subtypes (g), endothelial cell subtypes (h), mesenchymal cell subtypes (i). Different histological classifications (XGC, CC, LG, etc.) combined with different tissue sites (Pri, PO, LI, etc.) form more refined groups. For example, Adeno_Pri represents primary tumors of adenocarcinoma patients. For boxplots in c and d, the center line represents the median, box edges show quartiles, whiskers extend 1.5 times the interquartile range, and points beyond are individual outliers. n represents biologically independent samples.