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

Figure 3 Cell type-specific chromatin accessibility underlies functional diversity in hepatocellular carcinoma. A: Heatmap of 8780 cell type-specific accessible regions (columns) across cell types (rows). Z-score indicates accessibility deviation from mean; B: Pathway analysis of the single-cell RNA-sequencing marker for each cell type using the Kyoto Encyclopedia of Genes and Genomes pathway database. The score indicated normalized enrichment scores and q value denote Benjamini-Hochberg-adjusted P values; C: Pathway analysis of the single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq) marker peak enriched genes for each cell type using the Kyoto Encyclopedia of Genes and Genomes pathway database. The score indicated normalized enrichment scores and q value denote Benjamini-Hochberg-adjusted P values; D: Expression of scATAC-seq marker peak enriched genes in Liver Cancer Institute cohort grouped by cell peak. The upper panel shows the T-statistic from a paired t-test between tumor and adjacent non-tumor samples; E: Expression of scATAC-seq marker peak enriched genes in The Cancer Genome Atlas cohort grouped by cell peak. The upper panel shows the T-statistic from a paired t-test between tumor and adjacent non-tumor samples. FDR: False discovery rate; FC: Fold change; 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; KEGG: Kyoto Encyclopedia of Genes and Genomes; LCI: Liver Cancer Institute; TCGA: The Cancer Genome Atlas.