Fig. 2

Pateamine A identifies translated ORFs in lncRNAs. a, c Scatter plots of the translation efficiency (TE-) score versus the fraction of ribosome footprints that resist treatment with the translation inhibitors DMDA-PatA (A) and harringtonine (c). All annotated CDS (gray), annotated CDS smaller than 300 nucleotides (blue), snoRNAs (yellow) and lncRNAs (red). b, d Cumulative frequency distribution of the fraction of drug resistant ribosome footprints (B, pateamineA; D, harringtonine) for annotated protein coding sequences (black), annotated CDS smaller than 300 nucleotides (dark blue), range of scores or inhibition from 1000 bootstrappings of protein coding transcripts sampled to the same mRNA expression distribution as lncRNAs (light gray), all ORFs of lncRNAs (red), all ORFs of snoRNAs (yellow) and Refseq “other noncoding” RNAs (orange). e–g cumulative frequency plots for RR-score (e) ORF score (f) and Floss score (g) for the same subgroups of transcripts as in B and D. In A – G only data for transcripts with at least 20 transcriptome reads and more than 4 RNAse resistant footprints on the ORF are shown. ORFs on noncoding transcripts are only shown if at least 10 % of the RNAse resistant footprints of the transcript are located on the ORF to avoid analysis minor footprint peaks trailing major peaks. Noncoding RNAs that overlap annotated coding RNAs were excluded. h Pie charts showing the number of lncRNAs with ORFs that have: low footprint density ( TE score < 0.1, black); ORFs with below threshold number of ribosome footprints (<4 reads, gray); ribosome footprints on at least one ORF that are blocked at least 4 fold by pateamine (red), 2 fold by harringtonine (red), or both, at least 4 fold by DMDA-PatA and two fold by harringtonine (red); at least one ORF with above threshold number of ribosome footprints but no ORF with an above threshold effect of the translation inhibitors (blue). Only data for lncRNAs that have at least one ORF with at least 20 transcriptome reads are shown