Fig. 1: Transcriptomic diversity of liver cancer patients.

A t-SNE plot of all single cells from 15 primary liver cancer patients (indicated by colors). B Bubble chart shows the expression of canonical marker genes for annotating the cell types. C t-SNE plot of cell types from tumors (indicated by colors). Cells were annotated as T cells, B cells, TAFs, TAMs, LSECs, and HPC-like based on known lineage-specific marker genes (from B). The malignant cells were identified by infering CNV. D Stacked bar plots showing the cell composition of the 15 samples. E t-SNE plot of tumor cells from 15 tumors (indicated by colors). F Principal-component analysis (PCA) of tumor cells from 15 tumors. G PCA of tumor cells. Eigenvalue corresponding to each PC. H Transcriptomic diversity score of tumor samples according to the median value of diversity. Data are presented as the means ± SEM. I tumor cells t-SNE plot of tumor cells from the diversity-low (gray dots, L1-4) and diversity-high (red dots, H1-6) groups. J, K Pairwise correlation of all tumor cells from 15 liver cancer patients. Each pixel in the heatmap represents a correlation of two cells (the corresponding row and column). At least two independent experiments were performed for all data. For curve Figures and bar Figures, data are presented as means ± SD. Unpaired Student’s t-tests were used for comparing two variables. One-way ANOVA was used for multiple variables comparison.