Extended Data Fig. 9: Linking single-cell genotypes to their transcriptional phenotypes in in D3C2R1.
From: Deterministic evolution and stringent selection during preneoplasia
a, Inferred copy number heatmap from scRNA-seq data at day (d) 189, analogous to Fig. 6a. b, Fishplot schematic illustrating the link between lineage (ECBs) and copy number based subclones, similar to Fig. 6b. The actual subclone frequencies are shown in Fig. 5c. c, Scatterplot comparing subclone frequencies at day 157 and the fold change between days 129 and 157 for all subclones. Subclones of interest are highlighted as in panel A. d, Dotplot showing the expression of top differentially expressed genes (DEGs) based on GEPIA (gene expression profiling interactive analysis) of gastric cancer (GC). e, Volcano plot illustrating DEGs from the comparison of the winning subclone 0a and its parent subclone 0b. Vertical and horizontal lines correspond to absolute log2FC values of 1 and p-values < 0.00001 (Wilcoxon rank sum test, not corrected for multiple testing) respectively. f, GSEA heatmap from MSigDB Hallmark gene sets showing the most significantly altered pathways for the highlighted subclones (right; Kolmogorov-Smirnov statistic, Benjamini-Hochberg adjusted, two-sided). A manually reconstructed copy number phylogeny is shown above. The visualization is equivalent to Fig. 6f.
