title: NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events.
abstract: Nonsense-mediated decay (NMD) degrades mRNAs that include premature termination codons to avoid the translation and accumulation of truncated proteins. This mechanism has been found to participate in gene regulation and a wide spectrum of biological processes. However, the evolutionary and regulatory origins of NMD-targeted transcripts (NMDTs) have been less studied, partly because of the complexity in analyzing NMD events. Here we report NMD Classifier, a tool for systematic classification of NMD events for either annotated or de novo assembled transcripts. This tool is based on the assumption of minimal evolution/regulation-an event that leads to the least change is the most likely to occur. Our simulation results indicate that NMD Classifier can correctly identify an average of 99.3% of the NMD-causing transcript structural changes, particularly exon inclusions/exclusions and exon boundary alterations. Researchers can apply NMD Classifier to evolutionary and regulatory studies by comparing NMD events of different biological conditions or in different organisms.
authors.affiliation: Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu City, Taiwan.
authors.forename: Min-Kung
authors.initials: MK
authors.lastname: Hsu
authors.affiliation: Institute of Population Health Sciences, National Health Research Institutes, Zhunan Township, Miaoli County, Taiwan.
authors.forename: Hsuan-Yu
authors.initials: HY
authors.lastname: Lin
authors.affiliation: Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu City, Taiwan.|Institute of Population Health Sciences, National Health Research Institutes, Zhunan Township, Miaoli County, Taiwan.|School of Dentistry, China Medical University, Taichung City, Taiwan.
authors.forename: Feng-Chi
authors.identifier: http://orcid.org/0000-0002-1437-4420
authors.initials: FC
authors.lastname: Chen
mesh_terms: D000230:Adenocarcinoma / Q000378:metabolism; D000077192:Adenocarcinoma of Lung; D017398:Alternative Splicing; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D020407:Internet; D008175:Lung Neoplasms / Q000378:metabolism; D059365:Nonsense Mediated mRNA Decay