Fig 1.
The analysis flow of NMD Classifier.
Fig 2.
(a) The distribution of MCC values across different distances between a PTC and the last exon-exon junction. A positive (negative) distance indicates that the PTC is located upstream (downstream) of the last exon-exon junction; (b) False positive and false negative rates of different NMD prediction rule.
Fig 3.
(a) Distribution the accuracy of NMD Classifier in 1,000 simulation experiments. (b) The numbers of NMDTs identified in the transcriptomes of paired normal-tumor tissues from lung adenocarcinoma; the numbers in the parentheses indicate the percentages of NMDTs that are annotated by Ensembl; (c) The distribution of relative expression level (D value) of NMDTs between tumor and normal tissue.
Table 1.
An exemplar classification of NMD events in paired normal-tumor tissues from a lung adenocarcinoma patient.
Fig 4.
Alternative splicing events that result in NMDTs.
(a) Changes at exon boundaries; (b) inclusion or exclusion of one or more coding exons; (c) Intron retention. Changes in untranslated regions and complex NMD events are not shown here. The orange boxes indicate the exon groups identified to be the cause of NMD events. NMDT: NMD transcript; nNMDT: non-NMD transcript; A5SS/A3SS: alternative 5’/3’ splice site; A5SS-A3SS: exon boundary changes at both 5’ and 3’ ends; NMD_in/ NMD_ex: inclusion/exclusion of an exon causes the NMD event; multi_NMD_in/multi_NMD_ex) inclusion/exclusion of multiple exons causes the NMD event; NMD_IR/ nNMD_IR: intron retention in the NMDT/non-NMDT causes the NMD event; CDS: coding sequence; UTR: untranslated region.
Fig 5.
Examples of how NMD Classifier identifies NMD-causing event by calculating differences in reading frame between an NMDT and its best partner.
(a) Insertion of a single exon [exon group (ii)] causes a one-base frameshift and therefore an NMD event; (b) A one-base frameshift occurs at exon group (ii) but is offset downstream at group (iii). NMD Classifier thus continues to scan for the next frameshift event, which occurs at group (iv). This latter frameshift is maintained throughout to the stop codon, and is identified as the NMD-causing event.