NOA: a novel Network Ontology Analysis method
文献类型：期刊论文
| 作者 | Wang, Jiguang2; Huang, Qiang2; Liu, Zhi-Ping1; Wang, Yong2 ; Wu, Ling-Yun2; Chen, Luonan1,3; Zhang, Xiang-Sun2
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| 刊名 | NUCLEIC ACIDS RESEARCH
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| 出版日期 | 2011-07-01 |
| 卷号 | 39期号:13页码:12 |
| ISSN号 | 0305-1048 |
| DOI | 10.1093/nar/gkr251 |
| 英文摘要 | 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/. |
| 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 |
| 语种 | 英语 |
| WOS记录号 | WOS:000293020000004 |
| 出版者 | OXFORD UNIV PRESS |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/11831]  |
| 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. |
入库方式： OAI收割
来源：数学与系统科学研究院
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