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박시형
박시형 (Sihyung Park) 저자 이메일 보기
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조회 355  인쇄하기 주소복사 트위터 공유 페이스북 공유 
CLIPick: a sensitive peak caller for expression-based deconvolution of HITS-CLIP signals
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Abstract
High-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP, also called CLIP-Seq) has been used to map global RNA-protein interactions. However, a critical caveat of HITS-CLIP results is that they contain non-linear background noise-different extent of non-specific interactions caused by individual transcript abundance-that has been inconsiderately normalized, resulting in sacrifice of sensitivity. To properly deconvolute RNA-protein interactions, we have implemented CLIPick, a flexible peak calling pipeline for analyzing HITS-CLIP data, which statistically determines the signal-to-noise ratio for each transcript based on the expression-dependent background simulation. Comprising of streamlined Python modules with an easy-to-use standalone graphical user interface, CLIPick robustly identifies significant peaks and quantitatively defines footprint regions within which RNA-protein interactions were occurred. CLIPick outperforms other peak callers in accuracy and sensitivity, selecting the largest number of peaks particularly in lowly expressed transcripts where such marginal signals are hard to discriminate. Specifically, the application of CLIPick to Argonaute (Ago) HITS-CLIP data were sensitive enough to uncover extended features of microRNA target sites, and these sites were experimentally validated. CLIPick enables to resolve critical interactions in a wide spectrum of transcript levels and extends the scope of HITS-CLIP analysis. CLIPick is available at: http://clip.korea.ac.kr/clipick/
논문정보
- 형식: Research article
- 게재일: 2018년 10월 (BRIC 등록일 2018-10-31)
- 연구진: 국내연구진태극기
- 분야: Bioinformatics
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관련인물
안승현 (고려대학교)
조은솔 (고려대학교)
지성욱 (고려대학교)
관련분야 논문보기
Bioinformatics

외부링크
Google (by Sihyung Park)
Pubmed (by Sihyung Park)
프리미엄 Bio일정 Bio일정 프리미엄 안내
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장소: 아주대학교의료원 별관 대강당 (수원)
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초록접수: ~2018.12.31
사전접수: ~2018.12.31
날짜: 2019.04.24~26
장소: 이화여자대학교 삼성홀
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사전접수: ~2018.11.21
날짜: 2018.11.23
장소: 서울대학교병원 의생명연구원 1층 강당(대학로 소재)
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