Discovering microRNAs from deep sequencing data using miRDeep - PubMed (original) (raw)
Discovering microRNAs from deep sequencing data using miRDeep
Marc R Friedländer et al. Nat Biotechnol. 2008 Apr.
Abstract
The capacity of highly parallel sequencing technologies to detect small RNAs at unprecedented depth suggests their value in systematically identifying microRNAs (miRNAs). However, the identification of miRNAs from the large pool of sequenced transcripts from a single deep sequencing run remains a major challenge. Here, we present an algorithm, miRDeep, which uses a probabilistic model of miRNA biogenesis to score compatibility of the position and frequency of sequenced RNA with the secondary structure of the miRNA precursor. We demonstrate its accuracy and robustness using published Caenorhabditis elegans data and data we generated by deep sequencing human and dog RNAs. miRDeep reports altogether approximately 230 previously unannotated miRNAs, of which four novel C. elegans miRNAs are validated by northern blot analysis.
Similar articles
- Identification of plant microRNA homologs.
Dezulian T, Remmert M, Palatnik JF, Weigel D, Huson DH. Dezulian T, et al. Bioinformatics. 2006 Feb 1;22(3):359-60. doi: 10.1093/bioinformatics/bti802. Epub 2005 Nov 29. Bioinformatics. 2006. PMID: 16317073 - A comprehensive study of multiple mapping and feature selection for correction strategy in the analysis of small RNAs from SOLiD sequencing.
Guo L, Liang T, Lu Z. Guo L, et al. Biosystems. 2011 May-Jun;104(2-3):87-93. doi: 10.1016/j.biosystems.2011.01.004. Epub 2011 Jan 13. Biosystems. 2011. PMID: 21237247 - Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans.
Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP. Ruby JG, et al. Cell. 2006 Dec 15;127(6):1193-207. doi: 10.1016/j.cell.2006.10.040. Cell. 2006. PMID: 17174894 - Functional genomic, computational and proteomic analysis of C. elegans microRNAs.
Lehrbach NJ, Miska EA. Lehrbach NJ, et al. Brief Funct Genomic Proteomic. 2008 May;7(3):228-35. doi: 10.1093/bfgp/eln024. Epub 2008 Jun 19. Brief Funct Genomic Proteomic. 2008. PMID: 18565984 Review. - Computational analysis of small RNA cloning data.
Berninger P, Gaidatzis D, van Nimwegen E, Zavolan M. Berninger P, et al. Methods. 2008 Jan;44(1):13-21. doi: 10.1016/j.ymeth.2007.10.002. Methods. 2008. PMID: 18158128 Review.
Cited by
- Mechanisms underlying TRPV4-mediated regulation of miR-146a expression.
Dutta B, Mahanty M, Kesavalu L, Rahaman SO. Dutta B, et al. Front Immunol. 2024 Sep 30;15:1437540. doi: 10.3389/fimmu.2024.1437540. eCollection 2024. Front Immunol. 2024. PMID: 39403372 Free PMC article. - A pilot study of precision treatment for patients with lung cancer pain by Longteng Tongluo recipe using serum genomics.
Ruixin WU, Qingliang F, Sisi G, Xianglong W, Mengjun S, Zhujun M, Yabin G, Ling XU, Di Z, Changsheng D. Ruixin WU, et al. J Tradit Chin Med. 2024 Oct;44(5):1006-1016. doi: 10.19852/j.cnki.jtcm.20240828.005. J Tradit Chin Med. 2024. PMID: 39380232 Free PMC article. Clinical Trial. - A glimpse into the world of microRNAs and their putative roles in hard ticks.
Leal-Galvan B, Kumar D, Karim S, Saelao P, Thomas DB, Oliva Chavez A. Leal-Galvan B, et al. Front Cell Dev Biol. 2024 Sep 23;12:1460705. doi: 10.3389/fcell.2024.1460705. eCollection 2024. Front Cell Dev Biol. 2024. PMID: 39376631 Free PMC article. Review. - MiRNAs as potential biomarkers in early breast cancer detection: a systematic review.
Mihai AM, Ianculescu LM, Suciu N. Mihai AM, et al. J Med Life. 2024 Jun;17(6):549-554. doi: 10.25122/jml-2024-0322. J Med Life. 2024. PMID: 39296436 Free PMC article. - microRNA profile of endometrial cancer from Indian patients-identification of potential biomarkers for prognosis.
Hegde S, Wagh K, Narayana SM, Abikar A, Nambiar S, Ananthamurthy S, Narayana NH, Reddihalli PV, Chandraiah S, Ranganathan P. Hegde S, et al. Biochem Biophys Rep. 2024 Aug 25;39:101812. doi: 10.1016/j.bbrep.2024.101812. eCollection 2024 Sep. Biochem Biophys Rep. 2024. PMID: 39282095 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources