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dc.contributor.authorChou, Chih-Hungen_US
dc.contributor.authorLin, Feng-Maoen_US
dc.contributor.authorChou, Min-Teen_US
dc.contributor.authorHsu, Sheng-Daen_US
dc.contributor.authorChang, Tzu-Haoen_US
dc.contributor.authorWeng, Shun-Longen_US
dc.contributor.authorShrestha, Sirjanaen_US
dc.contributor.authorHsiao, Chiung-Chihen_US
dc.contributor.authorHung, Jui-Hungen_US
dc.contributor.authorHuang, Hsien-Daen_US
dc.date.accessioned2014-12-08T15:29:20Z-
dc.date.available2014-12-08T15:29:20Z-
dc.date.issued2013-01-21en_US
dc.identifier.issn1471-2164en_US
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2164-14-S1-S2en_US
dc.identifier.urihttp://hdl.handle.net/11536/21119-
dc.description.abstractBackground: MicroRNAs (miRNAs) play a critical role in down-regulating gene expression. By coupling with Argonaute family proteins, miRNAs bind to target sites on mRNAs and employ translational repression. A large amount of miRNA-target interactions (MTIs) have been identified by the crosslinking and immunoprecipitation (CLIP) and the photoactivatable-ribonucleoside-enhanced CLIP (PAR-CLIP) along with the next-generation sequencing (NGS). PAR-CLIP shows high efficiency of RNA co-immunoprecipitation, but it also lead to T to C conversion in miRNA-RNA-protein crosslinking regions. This artificial error obviously reduces the mappability of reads. However, a specific tool to analyze CLIP and PAR-CLIP data that takes T to C conversion into account is still in need. Results: We herein propose the first CLIP and PAR-CLIP sequencing analysis platform specifically for miRNA target analysis, namely miRTarCLIP. From scratch, it automatically removes adaptor sequences from raw reads, filters low quality reads, reverts C to T, aligns reads to 3'UTRs, scans for read clusters, identifies high confidence miRNA target sites, and provides annotations from external databases. With multi-threading techniques and our novel C to T reversion procedure, miRTarCLIP greatly reduces the running time comparing to conventional approaches. In addition, miRTarCLIP serves with a web-based interface to provide better user experiences in browsing and searching targets of interested miRNAs. To demonstrate the superior functionality of miRTarCLIP, we applied miRTarCLIP to two public available CLIP and PAR-CLIP sequencing datasets. miRTarCLIP not only shows comparable results to that of other existing tools in a much faster speed, but also reveals interesting features among these putative target sites. Specifically, we used miRTarCLIP to disclose that T to C conversion within position 1-7 and that within position 8-14 of miRNA target sites are significantly different (p value = 0.02), and even more significant when focusing on sites targeted by top 102 highly expressed miRNAs only (p value = 0.01). These results comply with previous findings and further suggest that combining miRNA expression and PAR-CLIP data can improve accuracy of the miRNA target prediction. Conclusion: To sum up, we devised a systematic approach for mining miRNA-target sites from CLIP-seq and PAR-CLIP sequencing data, and integrated the workflow with a graphical web-based browser, which provides a user friendly interface and detailed annotations of MTIs. We also showed through real-life examples that miRTarCLIP is a powerful tool for understanding miRNAs. Our integrated tool can be accessed online freely at http://miRTarCLIP.mbc.nctu.edu.tw.en_US
dc.language.isoen_USen_US
dc.titleA computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencingen_US
dc.typeArticle; Proceedings Paperen_US
dc.identifier.doi10.1186/1471-2164-14-S1-S2en_US
dc.identifier.journalBMC GENOMICSen_US
dc.citation.volume14en_US
dc.citation.issueen_US
dc.citation.epageen_US
dc.contributor.department生物科技學系zh_TW
dc.contributor.department生物資訊及系統生物研究所zh_TW
dc.contributor.departmentDepartment of Biological Science and Technologyen_US
dc.contributor.departmentInstitude of Bioinformatics and Systems Biologyen_US
dc.identifier.wosnumberWOS:000314471000002-
Appears in Collections:Conferences Paper


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