Fig. 5

Integrated analysis of gene expression, chromatin accessibility and chromosome conformation data. The profiles showing the normalized ATAC-seq tag density surrounding the center of the regions of A to B (A) and B to A (B) across a genomic window of ± 2 kb in mice with BLM-induced fibrosis, contrasted with the control. (C) The violin plot represents the log2 fold change (FC) between fibrosis and control for DEGs situated in regions associated with diverse compartmental switch categories. (D-E) Violin plot shows the expression levels [log2(FPKM + 1)] of DEGs found in regions associated with different compartmental switch categories. (F-G) Profiles illustrate the pattern of average PC1 values, as determined by the HOMER software (version 4.10), in the vicinity of the central areas of hyper- and hypo-accessible regions across a genomic span of ± 100 kb in BLM-induced fibrotic mice, contrasted with the control. (H) Scatter plot shows the correlation between the accessibility of chromatin and the expression of genes. ATAC-seq peaks with an adjusted p-value < 0.05 and genes found by RNA-seq with an adjusted p-value < 0.05 were plotted to analyze the variations in accessible peaks and gene expression. (I) Violin plot shows the log2 fold change (FC) between fibrosis and control for DEGs situated in regions linked to distinct accessible peaks. (J-K) Violin plot shows expression level [log2(FPKM + 1)] of DEGs residing at regions for different accessible peaks. (L-M) Profiles illustrate the distribution of average PC1 values surrounding the center of upregulated or downregulated genes across a genomic window of ± 100 kb in BLM-induced fibrotic mice compared to control. (N-O) The profiles present the normalized ATAC-seq tag density surrounding the center of the DEGs across a genomic window of ± 2 kb in BLM-induced fibrotic mice compared to control. (P) Venn diagram illustrates the distribution of gene categories in three different omics datasets. The overlapping areas represent genes common to multiple omics datasets, while distinct areas indicate unique genes within each dataset