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TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association

Title
TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association
Author
남진우
Keywords
LncRNA; LncRNA annotation; RNA binding protein association
Issue Date
2018-02
Publisher
BMC
Citation
BMC BIOINFORMATICS, v. 19, Article no. 41
Abstract
Background: LncRNAs are long regulatory non-coding RNAs, some of which are arguably predicted to have coding potential. Despite coding potential classifiers that utilize ribosome profiling data successfully detected actively translated regions, they are less sensitive to lncRNAs. Furthermore, lncRNA annotation can be susceptible to false positives obtained from 3' untranslated region (UTR) fragments of mRNAs. Results: To lower these limitations in lncRNA annotation, we present a novel tool TERIUS that provides a two-step filtration process to distinguish between bona fide and false lncRNAs. The first step successfully separates lncRNAs from protein-coding genes showing enhanced sensitivity compared to other methods. To eliminate 3' UTR fragments, the second step takes advantage of the 3' UTR-specific association with regulator of nonsense transcripts 1 (UPF1), leading to refined lncRNA annotation. Importantly, TERIUS enabled the detection of misclassified transcripts in published lncRNA annotations. Conclusions: TERIUS is a robust method for lncRNA annotation, which provides an additional filtration step for 3' UTR fragments. TERIUS was able to successfully re-classify GENCODE and miTranscriptome lncRNA annotations. We believe that TERIUS can benefit construction of extensive and accurate non-coding transcriptome maps in many genomes.
URI
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2013-9http://repository.hanyang.ac.kr/handle/20.500.11754/117456
ISSN
1471-2105
DOI
10.1186/s12859-018-2013-9
Appears in Collections:
COLLEGE OF NATURAL SCIENCES[S](자연과학대학) > LIFE SCIENCE(생명과학과) > Articles
COLLEGE OF NATURAL SCIENCES[S](자연과학대학) > LIFE SCIENCE(생명과학과) > Articles
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