Diagram of the algorithm steps to select candidate genes in a specific cell line. For simplification, we represent the emetine treatment and the analysis of only one gene in the flowchart, but the same filters and analysis should be applied for the actinomycin D treatment and for the rest of the genes. The initial step to select a candidate gene (Y gene) in a specific cell line (X cell line) is to obtain the detection called present “P,” absent “A,” or marginal “M” calculated by the GCOS software. This first filter allows selection of genes that are specifically down-regulated in one cell line in the presence of a functional NMD pathway (before drug treatment) compared to the other mock-treated cell lines. Afterward, the level of induction for each gene is quantified in each cell line, and these IRs are used to calculate the SR. This SR should allow differentiating between an induction due to stabilization of a transcript carrying a PTC in a specific cell line from a general transcriptional induction due to the drug treatment or because of the accumulation of common alternative splicings that could occur in several cell lines. We establish the arbitrary cutoff of SR more than 4. The final filter will select only genes that in addition to having a high SR in a specific cell line have an mRNA level that remains mainly unmodified after drug treatment in the other cell lines (IR= 06-1.7).