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

  • Song Qi
  • Shamima Akter
  • Song LiEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1933)


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.

Key words

Co-expression network lincRNA Noncoding RNA Plant 



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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Copyright information

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

Authors and Affiliations

  1. 1.Ph.D. Program in Genetics, Bioinformatics and Computational BiologyVirginia Polytechnic Institute and State UniversityBlacksburgUSA
  2. 2.Department of Crop & Soil Environmental SciencesVirginia Polytechnic Institute and State UniversityBlacksburgUSA

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