Fig. 3

Comparison of core promoter usage in translatome and transcriptome. a The percentage of genes using specific number of core promoters. b Scatterplot of the TC tag numbers in translatome and transcriptome. As the two axes are in logarithmic scale, the number of tags in all TCs has been increased by 1 to avoid 0. c Beanplot of the TC abundance measured by RPM. Among the TCs in transcriptome, those present in translatome are grouped into “Set A” while those not present are grouped into “Set B”. In this plot, the short green lines mark the observations of RPM, while the purple area shows the frequency of the observed RPM. The two long solid black lines stand for the average of each set and the long dotted black line stands for the overall average of two sets. d Correlation between TC fold change and TC shape class. The percentage (y-axis) of SP and BP classes is calculated with translatome-enriched TCs with minimal fold change on x-axis. The dashed grep line and yellow line stand for the percentage of SP and BP classes for translatome-depleted TCs with fold change < 0.5. e The consensus sequence of the immediate downstream 100 nt of the representative TSSs of the top-enriched 200 TCs, top-depleted 200 TCs and randomly picked 200 TCs. The three groups of 100-nt sequences were all analyzed with WebLogo. The x-axis shows the relative positions with respect to the representative TSS (at position 1)