Fig. 6

H3K4me3 and core promoter sequence are predictive of initiation directionality. Predicted vs. measured transcription directionality in H. sapiens a promoter and b enhancer regions showing significant forward and reverse initiation levels (n = 5231 and n = 1189, respectively) using a mixture linear model (left). Density plots of a promoter and b enhancer counts for different directionality groups predicted by the model (right). Models were trained on all promoter (a) and all enhancer (b) regions. Skewed (blue) and balanced (pink) directionality model components are displayed separately. c Tenfold cross-validation of three models including a model trained using core promoter sequence score ratios and H3K4me3 signal ratios, a model trained using core promoter sequence score ratios only and one trained using H3K4me3 ratios only. Boxplots show the correlation between predicted and measured transcription directionality for the test sets. Center line is the median, box represents the 25th and 75th percentiles and whiskers extend further by 1.58 times the interquartile distance divided by the square root of the number of data points. d Same as c but for enhancers