NOA: a novel Network Ontology Analysis method

doi:10.1093/nar/gkr251

CSpace > 应用数学研究所

	NOA: a novel Network Ontology Analysis method
	Wang, Jiguang 2; Huang, Qiang 2; Liu, Zhi-Ping 1; Wang, Yong2 ; Wu, Ling-Yun2 ; Chen, Luonan 1,3; Zhang, Xiang-Sun2
	2011-07-01
发表期刊	NUCLEIC ACIDS RESEARCH
ISSN	0305-1048
卷号	39 期号:13 页码:12
摘要	Gene ontology analysis has become a popular and important tool in bioinformatics study, and current ontology analyses are mainly conducted in individual gene or a gene list. However, recent molecular network analysis reveals that the same list of genes with different interactions may perform different functions. Therefore, it is necessary to consider molecular interactions to correctly and specifically annotate biological networks. Here, we propose a novel Network Ontology Analysis (NOA) method to perform gene ontology enrichment analysis on biological networks. Specifically, NOA first defines link ontology that assigns functions to interactions based on the known annotations of joint genes via optimizing two novel indexes 'Coverage' and 'Diversity'. Then, NOA generates two alternative reference sets to statistically rank the enriched functional terms for a given biological network. We compare NOA with traditional enrichment analysis methods in several biological networks, and find that: (i) NOA can capture the change of functions not only in dynamic transcription regulatory networks but also in rewiring protein interaction networks while the traditional methods cannot and (ii) NOA can find more relevant and specific functions than traditional methods in different types of static networks. Furthermore, a freely accessible web server for NOA has been developed at http://www.aporc.org/noa/.
DOI	10.1093/nar/gkr251
语种	英语
资助项目	NSFC[60873205] ; NSFC[10801131] ; NSFC[60970091] ; NSFC[61072149] ; NSFC[91029301] ; CAS[KSCX2-EW-R-01] ; SIBS from CAS[2009CSP002] ; Shanghai NSF[11ZR1443100] ; FIRST Program of Japan
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000293020000004
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/11832
专题	应用数学研究所
通讯作者	Chen, Luonan
作者单位	1.Chinese Acad Sci, Shanghai Inst Biol Sci, Key Lab Syst Biol, SIBS Novo Nordisk Translat Res Ctr PreDiabet, Shanghai 200233, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, Key Lab Management Decis & Informat Syst, Beijing 100190, Peoples R China 3.Univ Tokyo, Inst Ind Sci, Collaborat Res Ctr Innovat Math Modelling, Tokyo 1538505, Japan
推荐引用方式 GB/T 7714	Wang, Jiguang,Huang, Qiang,Liu, Zhi-Ping,et al. NOA: a novel Network Ontology Analysis method[J]. NUCLEIC ACIDS RESEARCH,2011,39(13):12.
APA	Wang, Jiguang.,Huang, Qiang.,Liu, Zhi-Ping.,Wang, Yong.,Wu, Ling-Yun.,...&Zhang, Xiang-Sun.(2011).NOA: a novel Network Ontology Analysis method.NUCLEIC ACIDS RESEARCH,39(13),12.
MLA	Wang, Jiguang,et al."NOA: a novel Network Ontology Analysis method".NUCLEIC ACIDS RESEARCH 39.13(2011):12.