Fig. 3

Inferred differentially expressed genes between COVID-19 patients with different outcomes were revealed by profiling cfDNA coverage in promoter regions. A The schematic illustration of deviation score for the quantification of relative transcriptional start site (TSS) coverage profile. The blue line represents the baseline, which is the mean of the relative coverage within ± 2 kb of TSS of nine healthy subjects. The red line represents the TSS coverage profile of a patient with COVID-19. The yellow-shaded areas represent the deviation between the TSS coverage profile of baseline and COVID-19 patients. Deviation score was calculated by accumulating the deviations within the shadow area. B Distribution of relative coverage deviations between COVID-19 patients and baseline across the TSS ± 2 kb region of the SIN3B gene. The blue and red lines indicate the average of deviation distributions for the alive and deceased groups, respectively. The shaded area flanking the average distributions represents the 95% confidence interval of the deviation values in each group. C The volcano plot for identifying TSSs with differential deviation scores (i.e., P-value < 0.001, | log2(fold change) | > 0.5) between alive and deceased COVID-19 groups. These TSSs are defined as DEG-TSS. D Box plots of the accumulated deviation scores (ADS) of 1,194 DEG-TSSs. E Enrichment analysis on pathway and biological process for 963 genes with DEG-TSSs. The top 20 pathways ranked by P-value are displayed