Fig. 1: Reanalysis of ribosome profiling datasets reveals patterns of ribosome occupancy.

a Heatmap (left panel) showing hierarchical clustering of 49 conditions of translation perturbation, based on the profiles of the polarity differences by comparing the treatment to the control groups. The 49 conditions were arranged by columns, and the 4842 transcripts were arranged by rows. The conditions of the second major cluster are listed to the right. The red arrows indicate the three RocA treatment conditions. The red asterisks indicate another two conditions of RocA. b Metagene plots of the averaged RPF read densities for all the transcripts (GSE70211). The X-axis represents the distance from the start codon (upper panel) and stop codon (lower panel). The transcripts used for the plot were 9712 (DMSO), 9429 (0.03 μM RocA), 8467 (0.3 μM RocA), and 8515 (3 μM RocA). c Boxplots showing the ratio of ribosome density at the first 75 codons over the whole CDS region, and the transcripts (n = 7007) used for analysis are the common ones for all samples in b. Center line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; points, outliers. d Volcano plot showing the results of differential expression analysis with the RPF reads from the ribosome profiling data. The significant p values are generated via DESeq2 and adjusted with the Benjamini and Hochberg method by default. Metagene plots showing ribosome distribution of the ERGs (e) and IRGs (f). Source data are provided as a Source Data file.