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. 2018 Apr 30;46(10):4893–4902. doi: 10.1093/nar/gky295

Figure 4.

Figure 4.

TGE scoring and validation. (A) Comparison of methods for confirming the identification of novel protein isoforms, applied to human PIT data. A set of 197 known isoforms found in the sample using PIT was used for validation. The scoring method can identify 76 of these as isoforms, which is an improvement over the 37 confirmed by the simple peptide evidence approach. (B) ROC curve showing performance of the scoring method in comparison to the traditional variant-specific peptide evidence based method for known isoforms. (C) The number of TGEs classified as isoform rapidly decreases as the threshold between TGE and reference score is increased, while the proportion of those that have been confirmed as isoforms present in the sample increases. (D) Comparison of isoform classification techniques applied on novel isoforms from all species. The scoring method predicts higher numbers of variant isoforms in the sample compared to the peptide evidence method, but misses some TGEs confirmed by peptide evidence. (E) Class distribution of TGEs confirmed by the scoring method for novel isoforms in human.