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Identification and function annotation of long intervening noncoding RNAs

文献类型：期刊论文

作者Luo, Haitao3,4; Bu, Dechao3; Sun, Liang3; Fang, Shuangsang3; Liu, Zhiyong1; Zhao, Yi2,3
刊名BRIEFINGS IN BIOINFORMATICS
出版日期2017-09-01
卷号18期号:5页码:789-797
ISSN号1467-5463
关键词transcriptom sequencing noncoding RNAs gene identification function annotation network analysis computational method
DOI10.1093/bib/bbw046
英文摘要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/.
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
语种英语
出版者OXFORD UNIV PRESS
WOS记录号WOS:000411516400008
源URL[http://119.78.100.204/handle/2XEOYT63/6757]  
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, Inst Comp Technol, Adv Comp Res Ctr, Beijing, 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.Chinese Acad Sci, Key Lab Intelligent Informat Proc, Inst Comp Technol, Beijing 100190, Peoples R China
4.Univ Chinese Acad Sci, Beijing 100190, 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.

入库方式： OAI收割

来源：计算技术研究所

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