Identification and function annotation of long intervening noncoding RNAs

doi:10.1093/bib/bbw046

	Identification and function annotation of long intervening noncoding RNAs
	Luo, Haitao 1,3; Bu, Dechao 1; Sun, Liang 1; Fang, Shuangsang 1; Liu, Zhiyong 4; Zhao, Yi 1,2
	2017-09-01
发表期刊	BRIEFINGS IN BIOINFORMATICS
ISSN	1467-5463
卷号	18 期号:5 页码:789-797
摘要	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 co-expression 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/.
关键词	transcriptom sequencing noncoding RNAs gene identification function annotation network analysis computational method
DOI	10.1093/bib/bbw046
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[31401119] ; National Natural Science Foundation of China[31371320] ; National Natural Science Foundation of China[61472397] ; National Natural Science Foundation of China[31501066]
WOS研究方向	Biochemistry & Molecular Biology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Mathematical & Computational Biology
WOS记录号	WOS:000411516400008
出版者	OXFORD UNIV PRESS
引用统计	被引频次：26[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/6758
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Zhao, Yi
作者单位	1.Chinese Acad Sci, Key Lab Intelligent Informat Proc, Inst Comp Technol, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Precis Med Ctr, Res Inst Informat Ind LuoYang, LuoYang Branch,Inst Comp Technol, Luoyang 471000, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100190, Peoples R China 4.Chinese Acad Sci, Inst Comp Technol, Adv Comp Res Ctr, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Luo, Haitao,Bu, Dechao,Sun, Liang,et al. Identification and function annotation of long intervening noncoding RNAs[J]. BRIEFINGS IN BIOINFORMATICS,2017,18(5):789-797.
APA	Luo, Haitao,Bu, Dechao,Sun, Liang,Fang, Shuangsang,Liu, Zhiyong,&Zhao, Yi.(2017).Identification and function annotation of long intervening noncoding RNAs.BRIEFINGS IN BIOINFORMATICS,18(5),789-797.
MLA	Luo, Haitao,et al."Identification and function annotation of long intervening noncoding RNAs".BRIEFINGS IN BIOINFORMATICS 18.5(2017):789-797.