Fig. 2

Validation of InSET method. a Density of positions and average depth of insertions in the exons of the CS > 0 and CS < 0 genes. b Average TPM of all CS > 0 or CS < 0 genes and of those with insertions in exons in the growth or drug survival challenge assays. c, d Density of positions and average depth of insertions in the exons of the SS ≤ 0 and SS > 0 lncRNAs (c) and in the various distance bins upstream or downstream of TSSs of the CS > 0 and CS < 0 genes (d). e Density of positions and average depth of insertions in the introns and not within ±10 kb region of TSSs of the CS > 0 and CS < 0 genes. f Average TPM of all genes and those with IACFs in exons. For average and median depth of insertions, insertion positions with insertion number greater than or equal to 10,000 were removed as outliers to avoid the bias. For density of positions and average depth of insertions, error bars indicate the SD based on 5 K562 sample types. For average TPM, error bars indicate SD of 2 biological replicates. Red asterisks indicate significant differences under two-sided paired Student’s t test (p value < 0.05). Black asterisk indicates p value = 0.05. Source data are provided in Additional file 2: Tables S1-S3