Fig. 1: Estimation of translated isoforms.

a Diagram of the ORQAS pipeline. b Uniformity (x-axis) and periodicity (y-axis) for all tested ORFs with RNA expression TPM >0.1 and ≥10 Ribo-seq reads assigned (yellow) from human glia (n = 28,427). Uniformity is the percentage of maximum entropy, and periodicity is measured in the first annotated frame. In blue, single-ORF genes with protein expression in 37 tissues from the Human Protein Atlas (THPA). Other samples are shown in Supplementary Fig. 1. c ORQAS predictions in human glia for 1005 single-ORF genes. The plot shows the protein expression from immunohistochemistry (IHC) experiments in human cortex from THPA for cases without enough RNA expression (Not evaluated n = 468), cases that do not pass the filters of uniformity and periodicity (Not-translated n = 176), and those predicted to be translated (n = 361). d Number of ORFs translated per sample, according to whether the ORF is encoded by a single-ORF gene (Single), the most abundant isoform according to RNA-seq (Main isoform), the second most abundant (Secondary isoform), or by any of the remaining isoforms (Other isoforms). Tested ORFs that are not-translated are depicted in gray (Not-translated). e Average density of Ribo-seq reads along ORFs in the single-ORF genes from above, in ORFs from the most abundant isoform according to RNA-seq, and in the second most abundant isoform. f Number of ORFs translated per gene in human glia (hsa glia) according to ORQAS (orange) and ORFquant (yellow) predictions. Other samples are shown in Supplementary Fig 6. g Correlation between average ORF abundance in ribosome space for human glia (hsa glia n = 53,403) in ORFs per million (OPM) by ORQAS and P sites per nucleotide per million (P sites pNpM) by ORFquant, indicating whether each ORF is predicted only by ORQAS (orange) or by ORFquant (yellow), by both (blue), or none of them (gray). Other samples are shown in Supplementary Fig 8. h Distribution of the average RNA expression in human glia (has glia n = 30,035) in TPM for ORFs predicted only by ORQAS (orange), by ORFquant (yellow) or by both (blue). Other samples are shown in Supplementary Fig. 9.