Chromatin accessibility module identified by single-cell sequencing underlies the diagnosis and prognosis of hepatocellular carcinoma

Figure 4 Malignant cells harbored multiple enhancer-like peaks driving oncogenic transcription. A: Row scaled heatmaps of statistically significant peak-to-gene (P2G) links. Each row represents expression of a gene (left) correlated to chromatin accessibility of a peak (right); B: Overlap between P2G links and cell type-specific accessible regions; C: Stacked bar plot showing P2G uniquely related to specific marker across cell type. Malignant cells exhibit the highest regulatory complexity; D: Stacked bar plot showing number of genes per peak linked to across cell type. Malignant peaks target more genes (P < 0.001); E: Correlation coefficients (Pearson r) of P2G links across cell types. Malignant cells display stronger correlations (P < 0.001); F: Gene ontology enrichment analysis of the P2G enriched genes for each cell type. The score indicated normalized enrichment scores and q value denote benjamini-hochberg-adjusted P values; G: Browser track showing the accessibility profile at the strongest peak locus across all cell types (chr8 144286909-144366910). Peak was further highlighted by light red shallows; H: Uniform manifold approximation and projection plots of 15660 single-cell RNA-sequencing cells color-coded expression of the strongest peak hub. scRNA-seq: Single-cell RNA-sequencing; ATAC-seq: Assay for transposase-accessible chromatin using sequencing; scATAC-seq: Single-cell assay for transposase-accessible chromatin with sequencing; P2G: Peak-to-gene; UMAP: Uniform manifold approximation and projection;