Fig. 4

Analysis of degradation of cryptic unstable transcripts (CUTs) and stable unannotated transcripts (SUTs). a The log2 scaled ratio of CUTs fragments per kilobase per million reads (FPKM) normalized to the steady state (SS) levels. These ratios were used to quantify the degradation rate. A weighted average of the three nascent ratios was used to quantify the degradation rate, that is, the higher the ratio at the nascent points, the faster the degradation. b Comparison of features between the fastest-degrading third and slowest-degrading third of CUTs/SUTs. Features include average secondary structure free folding energy for each nucleotide, and transcript length. c SUTs are significantly longer than CUTs. Comparison of CUT and SUT transcript length distribution using the Kolmogorov–Smirnov (K–S) test. d The binary classification between the fastest-degrading third of transcripts and the slowest-degrading third of transcripts using ΔG per nucleotide (nt), transcript length, ΔG of ±15 nt around the start site and ΔG of ±15 nt around the stop site. The receiver operating characteristic (ROC) curves shows the data for the CUTs, SUTs or both with 10-folder cross-validation via a naive Bayes classifier. The area under the curve (AUC) is used to represent the prediction performance