Fig. 4: Key transcription factors (TFs) identified by ATAC-seq.

A Heatmap of differentially expressed open chromatin regions detected by ATAC-seq and grouped by RNA-seq-based subgroups. B Bubble plots represent TFs significantly enriched for genes with differentially expressed ATAC-seq peaks (Fisher’s exact test). C Network of significantly enriched TFs with target genes, whose expression levels were determined according to RNA-seq results. D Boxplots presenting gene expression in patients with transcriptional activity of TFPA2C (Positive n = 20, Negative n = 48) and XRCC5 (Positive n = 34, Negative n = 34) by two-tailed Student’s t-test. Pearson correlations between gene expression and transcriptional activity greater than 0.3 were present. Transcriptional activity was represented by the normalized enrichment score from the single-sample gene set enrichment analysis method. Boxplot shows the median (center line), 25th, and 75th percentiles (lower and upper boundaries). The upper whisker extends from the upper boundary to the maxima value no further than 1.5 × IQR from the boundary. The lower whisker extends from the lower boundary to the minima value at most 1.5×IQR of the boundary. Data beyond the end of the whiskers are outlying points and are plotted individually. ATAC-seq, assay for transposase-accessible chromatin sequencing, OS overall survival; AFP alpha fetal protein, IQR interquartile range.