ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs

doi:10.1093/nar/gkab435

	ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs
	Zhang, Yuwei 1,2; Bu, Dechao 3; Huo, Peipei 4; Wang, Zhihao 4; Rong, Hao 1,2; Li, Yanguo 5; Liu, Jingjia 6; Ye, Meng 1; Wu, Yang 3; Jiang, Zheng 7; Liao, Qi 1,2; Zhao, Yi 3
	2021-07-02
发表期刊	NUCLEIC ACIDS RESEARCH
ISSN	0305-1048
卷号	49 期号:W1 页码:W459-W468
摘要	Increasing evidence proves the essential regulatory roles of non-coding RNAs (ncRNAs) in biological processes. However, characterizing the specific functions of ncRNAs remains a challenging task, owing to the intensive consumption of the experimental approaches. Here, we present an online platform ncFANs v2.0 that is a significantly enhanced version of our previous ncFANs to provide multiple computational methods for ncRNA functional annotation. Specifically, ncFANs v2.0 was updated to embed three functional modules, including ncFANs-NET, ncFANs-eLnc and ncFANs-CHIP. ncFANs-NET is a new module designed for data-free functional annotation based on four kinds of pre-built networks, including the co-expression network, co-methylation network, long non-coding RNA (lncRNA)-centric regulatory network and random forest-based network. ncFANs-eLnc enables the one-stop identification of enhancer-derived lncRNAs from the de novo assembled transcriptome based on the user-defined or our pre-annotated enhancers. Moreover, ncFANs-CHIP inherits the original functions for microarray data-based functional annotation and supports more chip types. We believe that our ncFANs v2.0 carries sufficient convenience and practicability for biological researchers and facilitates unraveling the regulatory mechanisms of ncRNAs. The ncFANs v2.0 server is freely available at http://bioinfo.org/ncfans or http://ncfans.gene.ac.
DOI	10.1093/nar/gkab435
收录类别	SCI
语种	英语
资助项目	CAMS Innovation Fund for Medical Sciences (CIFMS)[2019-I2M-2-002] ; CAMS Innovation Fund for Medical Sciences (CIFMS)[2017-I2M-1-006] ; Natural Science Foundation of Zhejiang Province[LY21C060002] ; Fundamental Research Funds for the Provincial Universities of Zhejiang[SJLZ2021001] ; National Natural Science Foundation of China[31970630] ; Zhejiang Key Laboratory of Pathophysiology[201812] ; Zhejiang Provincial Research Center for Cancer Intelligent Diagnosis and Molecular Technology[JBZX-202003] ; K. C. Wong Magna Fund in Ningbo University
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000672775800059
出版者	OXFORD UNIV PRESS
引用统计	被引频次：13[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/2XEOYT63/17492
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Liao, Qi; Zhao, Yi
作者单位	1.Ningbo Univ, Med Sch, Affiliated Hosp, Ningbo 315000, Zhejiang, Peoples R China 2.Ningbo Univ, Sch Med, Dept Preventat Med, Zhejiang Prov Key Lab Pathol & Physiol Technol, Ningbo 315000, Zhejiang, Peoples R China 3.Chinese Acad Sci, Pervas Comp Res Ctr, Inst Comp Technol, Beijing 100190, Peoples R China 4.Chinese Acad Sci, Luoyang Branch, Inst Comp Technol, Luoyang 471000, Henan, Peoples R China 5.Ningbo Univ, Inst Drug Discovery Technol, Ningbo 315000, Zhejiang, Peoples R China 6.Univ Chinese Acad Sci, Ningbo Inst Life & Hlth Ind, Ningbo 315000, Zhejiang, Peoples R China 7.Chinese Acad Med Sci & Peking Union Med Coll, Canc Hosp, Natl Clin Res Ctr Canc, Dept Colorectal Surg,Natl Canc Ctr, Beijing 100021, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Yuwei,Bu, Dechao,Huo, Peipei,et al. ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs[J]. NUCLEIC ACIDS RESEARCH,2021,49(W1):W459-W468.
APA	Zhang, Yuwei.,Bu, Dechao.,Huo, Peipei.,Wang, Zhihao.,Rong, Hao.,...&Zhao, Yi.(2021).ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs.NUCLEIC ACIDS RESEARCH,49(W1),W459-W468.
MLA	Zhang, Yuwei,et al."ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs".NUCLEIC ACIDS RESEARCH 49.W1(2021):W459-W468.