NPInter v3.0: an upgraded database of noncoding RNA-associated interactions

doi:10.1093/database/baw057

	NPInter v3.0: an upgraded database of noncoding RNA-associated interactions
	Hao, Yajing 1,2,3; Wu, Wei 1,2,3; Li, Hui 3,4; Yuan, Jiao 1,2,3; Luo, Jianjun 1,2; Zhao, Yi 4; Chen, Runsheng 1,2
	2016-04-17
发表期刊	DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
ISSN	1758-0463
页码	9
摘要	Despite the fact that a large quantity of noncoding RNAs (ncRNAs) have been identified, their functions remain unclear. To enable researchers to have a better understanding of ncRNAs' functions, we updated the NPInter database to version 3.0, which contains experimentally verified interactions between ncRNAs (excluding tRNAs and rRNAs), especially long noncoding RNAs (lncRNAs) and other biomolecules (proteins, mRNAs, miRNAs and genomic DNAs). In NPInter v3.0, interactions pertaining to ncRNAs are not only manually curated from scientific literature but also curated from high-throughput technologies. In addition, we also curated lncRNA-miRNA interactions from in silico predictions supported by AGO CLIP-seq data. When compared with NPInter v2.0, the interactions are more informative (with additional information on tissues or cell lines, binding sites, conservation, co-expression values and other features) and more organized (with divisions on data sets by data sources, tissues or cell lines, experiments and other criteria). NPInter v3.0 expands the data set to 491,416 interactions in 188 tissues (or cell lines) from 68 kinds of experimental technologies. NPInter v3.0 also improves the user interface and adds new web services, including a local UCSC Genome Browser to visualize binding sites. Additionally, NPInter v3.0 defined a high-confidence set of interactions and predicted the functions of lncRNAs in human and mouse based on the interactions curated in the database. NPInter v3.0 is available at http://www.bioinfo.org/NPInter/.
DOI	10.1093/database/baw057
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[31520103905] ; National Natural Science Foundation of China[31371320] ; National Natural Science Foundation of China[31401119] ; National High Technology Research and Development Program ('863' Program) of China[2015AA020108] ; National High Technology Research and Development Program ('863' Program) of China[2014AA021103] ; National High Technology Research and Development Program ('863' Program) of China[2014AA021502] ; Training Program of the Major Research Plan of the National Natural Science Foundation of China[91229120] ; Chinese Academy of Science Strategic Project of Leading Science and Technology[XDA01020402]
WOS研究方向	Mathematical & Computational Biology
WOS类目	Mathematical & Computational Biology
WOS记录号	WOS:000374650100002
出版者	OXFORD UNIV PRESS
引用统计	被引频次：104[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/2XEOYT63/8502
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; Chen, Runsheng
作者单位	1.Chinese Acad Sci, Inst Biophys, Key Lab RNA Biol, Beijing 100101, Peoples R China 2.Chinese Acad Sci, Inst Biophys, Beijing Key Lab Noncoding RNA, Beijing 100101, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Chinese Acad Sci, Bioinformat Res Grp, Key Lab Intelligent Informat Proc, Adv Comp Res Ctr,Inst Comp Technol, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Hao, Yajing,Wu, Wei,Li, Hui,et al. NPInter v3.0: an upgraded database of noncoding RNA-associated interactions[J]. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION,2016:9.
APA	Hao, Yajing.,Wu, Wei.,Li, Hui.,Yuan, Jiao.,Luo, Jianjun.,...&Chen, Runsheng.(2016).NPInter v3.0: an upgraded database of noncoding RNA-associated interactions.DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION,9.
MLA	Hao, Yajing,et al."NPInter v3.0: an upgraded database of noncoding RNA-associated interactions".DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2016):9.