Fig. 3

ARTDeco successfully discriminates between genes that are directly induced by IAV infection (primary induction) and genes induced as a results of readthrough transcription (read-in). a Heatmap of z-normalized expression values and ARTDeco assignments for gold standard primary induction and read-in genes. Thresholds for assigning read-in genes were log2 fold change > 2, adjusted p-value < 0.05, and read-in level > − 2. Leftmost column is ARTDeco assignment (blue is primary induction and red is read-in). Next column is gold standard assignment (green is primary induction and gold is read-in). Remaining columns are z-normalized gene expression for IAV replicate 1, IAV replicate 2, ΔNS1 replicate 1, ΔNS1 replicate2, mock replicate 1, and mock replicate 2. b Distribution of log2 ratio of H3K27ac for IAV vs. Mock conditions at promoters for primary induction and read-in genes. (p < 1e-20; t-test) c Distribution of log2 ratio of H3K4me3 for IAV vs. Mock conditions at promoters for primary induction and read-in genes. (p < 1e-10; t-test) d Distribution of RNA PolII serine-2 phosphorylation (S2p) at promoters in the IAV condition for primary induction and read-in genes. (p < 0.001; t-test) e Distribution of RNA PolII serine-5 phosphorylation (S5p) in the IAV condition at promoters for primary induction and read-in genes. (p < 1e-5; t-test) f Distribution of log2 ratio of Start-seq signal for IAV vs. Mock at promoters for primary induction and read-in genes. (p < 1e-14; t-test)