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deepBase: Annotation and Discovery of MicroRNAs and Other Noncoding RNAs from Deep-Sequencing Data

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Next-Generation MicroRNA Expression Profiling Technology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 822))

Abstract

Recent advances in high-throughput deep-sequencing technology have produced large numbers of short and long RNA sequences and enabled the detection and profiling of known and novel microRNAs (miRNAs) and other noncoding RNAs (ncRNAs) at unprecedented sensitivity and depth. In this chapter, we describe the use of deepBase, a database that we have developed to integrate all public deep-sequencing data and to facilitate the comprehensive annotation and discovery of miRNAs and other ncRNAs from these data. deepBase provides an integrative, interactive, and versatile web graphical interface to evaluate miRBase-annotated miRNA genes and other known ncRNAs, explores the expression patterns of miRNAs and other ncRNAs, and discovers novel miRNAs and other ncRNAs from deep-sequencing data. deepBase also provides a deepView genome browser to comparatively analyze these data at multiple levels. deepBase is available at http://deepbase.sysu.edu.cn/.

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Acknowledgments

This research is supported by the National Natural Science Foundation of China (No. 30830066, 30900820); Ministry of Science and Technology of China, National Basic Research Program (No. 2005CB724600, 2011CB811300); the funds from the Ministry of Education of China and Guangdong Province (No. 9451027501002591); and China Postdoctoral Science Foundation (No. 200902348).

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Authors and Affiliations

  1. Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, P.R. China

    Jian-Hua Yang & Liang-Hu Qu

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  1. Jian-Hua Yang
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  2. Liang-Hu Qu
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Corresponding author

Correspondence to Liang-Hu Qu .

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Editors and Affiliations

  1. Illumina, Inc., Towne Centre Drive 9885, San Diego, 92121, California, USA

    Jian-Bing Fan

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Yang, JH., Qu, LH. (2012). deepBase: Annotation and Discovery of MicroRNAs and Other Noncoding RNAs from Deep-Sequencing Data. In: Fan, JB. (eds) Next-Generation MicroRNA Expression Profiling Technology. Methods in Molecular Biology, vol 822. Humana Press. https://doi.org/10.1007/978-1-61779-427-8_16

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  • DOI: https://doi.org/10.1007/978-1-61779-427-8_16

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-426-1

  • Online ISBN: 978-1-61779-427-8

  • eBook Packages: Springer Protocols

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