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

Song Qi; Shamima Akter; Song Li

doi:10.1007/978-1-4939-9045-0_12

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

Methods Mol Biol. 2019:1933:207-221. doi: 10.1007/978-1-4939-9045-0_12.

Authors

Song Qi^{1

2}, Shamima Akter², Song Li³

Affiliations

¹ Ph.D. Program in Genetics, Bioinformatics and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
² Department of Crop & Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
³ Department of Crop & Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA. songli@vt.edu.

PMID: 30945187
DOI: 10.1007/978-1-4939-9045-0_12

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.

Keywords: Co-expression network; Noncoding RNA; Plant; lincRNA.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Arabidopsis / genetics*
Computational Biology / methods
DNA, Intergenic / genetics*
Gene Expression Regulation, Plant*
Gene Regulatory Networks*
High-Throughput Nucleotide Sequencing / methods*
RNA, Long Noncoding / genetics*
RNA, Plant / genetics*
Transcriptome

Substances

DNA, Intergenic
RNA, Long Noncoding
RNA, Plant