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Identification of Novel lincRNA and Co-Expression Network Analysis Using RNA-Sequencing Data in Plants

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Plant Long Non-Coding RNAs

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1933))

Abstract

Long intergenic noncoding RNA (lincRNA) plays important biological functions in plants. Identification and annotation of lincRNA in plants largely rely on RNA sequencing followed by computational analysis. In this protocol, we describe a multistep computational pipeline for lincRNA identification using RNA-sequencing data. This pipeline can also construct co-expression network that is made of both lincRNA and mRNA genes. The co-expression network generated by this pipeline can be used to provide putative annotation of lincRNAs that have no known biological functions.

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Acknowledgment

This work is supported by the Virginia Agricultural Experiment Station (Blacksburg) and the National Institute of Food and Agriculture, US Department of Agriculture (Washington, DC).

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Authors and Affiliations

  1. Ph.D. Program in Genetics, Bioinformatics and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA

    Song Qi

  2. Department of Crop & Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA

    Song Qi, Shamima Akter & Song Li

Authors
  1. Song Qi
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  2. Shamima Akter
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  3. Song Li
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Corresponding author

Correspondence to Song Li .

Editor information

Editors and Affiliations

  1. Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China

    Julia A. Chekanova  & Hsiao-Lin V. Wang  & 

  2. Department of Biology, Emory University, Atlanta, Georgia, USA

    Hsiao-Lin V. Wang

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© 2019 Springer Science+Business Media, LLC, part of Springer Nature

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Qi, S., Akter, S., Li, S. (2019). Identification of Novel lincRNA and Co-Expression Network Analysis Using RNA-Sequencing Data in Plants. In: Chekanova, J.A., Wang, HL.V. (eds) Plant Long Non-Coding RNAs. Methods in Molecular Biology, vol 1933. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9045-0_12

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  • DOI: https://doi.org/10.1007/978-1-4939-9045-0_12

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9044-3

  • Online ISBN: 978-1-4939-9045-0

  • eBook Packages: Springer Protocols

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