Luo Haitao, Bu Dechao, Sun Liang, Fang Shuangsang, Liu Zhiyong, Zhao Yi
Brief Bioinform. 2017 Sep 1;18(5):789-797. doi: 10.1093/bib/bbw046.
RNA-seq technology offers the promise of rapid comprehensive discovery of long intervening noncoding RNAs (lincRNAs). Basic tools such as Tophat and Cufflinks have been widely used for RNA-seq assembly. However, advanced bioinformatics methodologies that allow in-depth analysis of lincRNAs are lacking. Here, we describe a computational protocol that is especially designed for the identification of novel lincRNAs and the prediction of the function. The protocol mainly includes two open-access tools, CNCI and ncFANs. CNCI allows users to distinguish noncoding from protein-coding transcripts and to retrieve novel lincRNAs. ncFANs integrates expression profiles of protein-coding and lincRNA genes to construct coexpression networks. Such networks are subsequently used to perform function predictions of unknown lincRNAs. This protocol will allow users to apply these procedures without the need of additional training. All the tools in current protocol are available http://www.bioinfo.org/np/.
RNA测序技术有望快速全面地发现长链居间非编码RNA（lincRNA）。诸如Tophat和Cufflinks等基础工具已被广泛用于RNA测序组装。然而，目前缺乏能够对lincRNA进行深入分析的先进生物信息学方法。在此，我们描述了一种专门设计用于鉴定新型lincRNA和预测其功能的计算方案。该方案主要包括两个开放获取工具，即CNCI和ncFANs。CNCI可让用户区分非编码转录本和蛋白质编码转录本，并检索新型lincRNA。ncFANs整合蛋白质编码基因和lincRNA基因的表达谱以构建共表达网络。随后利用这些网络对未知lincRNA进行功能预测。该方案将使用户无需额外培训即可应用这些程序。当前方案中的所有工具均可从http://www.bioinfo.org/np/获取。
