Fig. 4

uORFs shift translationally with Retinoic acid induced differentiation. a K-means clustering analysis of log₂(uORF TE) in Non-Diff and RA-Diff cells, reveals differentiation-associated shifts. Three clusters of uORF translation emerge: those that are up-regulated in RA-Diff cells (cyan), up-regulated in Non-Diff cells (gold), and uORFs with no change in translational potential (gray). b Clustering in (A) does not correlate with directional CDS changes. Kernel density estimation analysis of changes in TPM over annotated protein-coding CDS as a function of changes in TPM over predicted upstream-initiated ORFs. Cluster identity of predicted ORF changed in translational potential as scored by SPECtre predicted ORFs enriched for translation in RA-Diff cells (cyan), predicted ORFs with enriched translation in Non-Diff cells (gold), and those with static translation across the two conditions (black) are annotated to protein-coding CDS with higher RPF abundance in Non-Diff cells (above horizontal line), and those with higher RPF abundance in RA-Diff cells (below horizontal line). c Analysis of transcripts with a cORF reveals a positive correlation of cORF TE and CDS TE. Pearson correlation, R² = 0.13. d The same is true for oORFs with a Pearson correlation, R² = 0.59.