NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events Article Swipe
Min-Kung Hsu
,
Hsuan‐Yu Lin
,
Feng‐Chi Chen
·
YOU?
·
· 2017
· Open Access
·
· DOI: https://doi.org/10.1371/journal.pone.0174798
YOU?
·
· 2017
· Open Access
·
· DOI: https://doi.org/10.1371/journal.pone.0174798
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.
Related Topics
Concepts
Nonsense-mediated decay
Classifier (UML)
Biology
Computational biology
Exon
Genetics
Gene
Computer science
Artificial intelligence
RNA
RNA splicing
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1371/journal.pone.0174798
- https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0174798&type=printable
- OA Status
- gold
- Cited By
- 52
- References
- 37
- Related Works
- 10
- OpenAlex ID
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All OpenAlex metadata
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- DOI
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https://doi.org/10.1371/journal.pone.0174798Digital Object Identifier
- Title
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NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay eventsWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2017Year of publication
- Publication date
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2017-04-03Full publication date if available
- Authors
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Min-Kung Hsu, Hsuan‐Yu Lin, Feng‐Chi ChenList of authors in order
- Landing page
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https://doi.org/10.1371/journal.pone.0174798Publisher landing page
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https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0174798&type=printableDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0174798&type=printableDirect OA link when available
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Nonsense-mediated decay, Classifier (UML), Biology, Computational biology, Exon, Genetics, Gene, Computer science, Artificial intelligence, RNA, RNA splicingTop concepts (fields/topics) attached by OpenAlex
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52Total citation count in OpenAlex
- Citations by year (recent)
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2025: 4, 2024: 12, 2023: 5, 2022: 7, 2021: 6Per-year citation counts (last 5 years)
- References (count)
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37Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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