Fig. 6
Validation of the FLT-based ORFeome using MS-based proteomics. a Bar plots show the number (left) and percentage (right) of ORFs supported with peptide evidence. Except for the RefSeq-annotated ORFs where all peptides were used, in the other ORF categories only the FLT-specific peptides were used. N-terminal truncation and internal deletion were excluded since no FLT-specific peptides were expected. b Boxplots compare the ORFscores of ORFs with peptide evidence to those without in each category. P values (Mann–Whitney U test) are indicated above the boxplots. Box edges represent quartiles, whiskers represent extreme data points no more than 1.5 times the interquartile range. c, d Two examples of peptide-supported novel ORFs identified in the known gene loci. Tracks from top to bottom are genomic coordinates, two replicates of ribosome-free RNA, two replicates of monosome-associated RNA, two replicates of polysome-associated RNA, two replicates of ribosome footprinting, PhyloP conservation score, peptide evidence, full-length transcripts, and RefSeq genes. Zoomed-in regions are also shown at the bottom, with the same track orders. c In the gene Rpp14, peptide evidence was only found in the novel ORF in its 3′UTR, whereas d in the gene Nudt13, peptide evidence was found for both the RefSeq-annotated main ORF and the novel ORF in its 3´UTR. Source data for panel b are provided in a Source Data file
