A Network Biology Study on Circadian Rhythm by Integrating Various Omics Data

doi:10.1089/omi.2009.0040

CSpace > 应用数学研究所

	A Network Biology Study on Circadian Rhythm by Integrating Various Omics Data
	Wang, Yong1 ; Zhang, Xiang-Sun1 ; Chen, Luonan 2,3
	2009-08-01
发表期刊	OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
ISSN	1536-2310
卷号	13 期号:4 页码:313-324
摘要	Circadian rhythm is fundamentally important in physiological processes of mammals. To reveal its underlying mechanism, we probed functional interactions among genes, motivated by the basic molecular observation on gene expression data in circadian rhythm that a large number of genes oscillate in a coordinated manner. In this study, a reverse-engineering strategy was applied to infer and analyze the structure and function of a circadian rhythm-related gene regulatory network. Specifically, our method integrated four phase-shift time-course gene expression datasets in rat suprachiasmatic nucleus, protein-protein interactions, phosphorylations of a set of key circadian genes, and prior information of cis-regulatory elements, to construct the gene regulatory network related to circadian rhythm of the rat. By follow-up analysis, we identified four new regulatory hubs that may play crucial roles in the regulation of circadian rhythm. Furthermore, we found that feedback loop motifs were significantly enriched in the predicted network, which may contribute to the genome-wide oscillations of the circadian clock. Compared to the small-scale gene regulatory network conducted by experimental method, our study provides a system-wide overview on the gene regulations, which not only reveals the global network structure but also gives valuable insights into the essential mechanism of circadian rhythm.
DOI	10.1089/omi.2009.0040
语种	英语
资助项目	National Natural Science Foundation of China[10801131] ; National Natural Science Foundation of China[10631070] ; Chinese Academy of Sciences ; JSPS ; NSFC
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:000270328000004
出版者	MARY ANN LIEBERT, INC
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/7258
专题	应用数学研究所
通讯作者	Wang, Yong
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 2.Osaka Sangyo Univ, Dept Elect Informat & Commun, Osaka 5748530, Japan 3.Shanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
推荐引用方式 GB/T 7714	Wang, Yong,Zhang, Xiang-Sun,Chen, Luonan. A Network Biology Study on Circadian Rhythm by Integrating Various Omics Data[J]. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY,2009,13(4):313-324.
APA	Wang, Yong,Zhang, Xiang-Sun,&Chen, Luonan.(2009).A Network Biology Study on Circadian Rhythm by Integrating Various Omics Data.OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY,13(4),313-324.
MLA	Wang, Yong,et al."A Network Biology Study on Circadian Rhythm by Integrating Various Omics Data".OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 13.4(2009):313-324.