Inferring gene regulatory networks from multiple microarray datasets

doi:10.1093/bioinformatics/btl396

CSpace > 应用数学研究所

	Inferring gene regulatory networks from multiple microarray datasets
	Wang, Yong ; Joshi, Trupti ; Zhang, Xiang-Sun; Xu, Dong ; Chen, Luonan
	2006-10-01
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	22 期号:19 页码:2413-2420
摘要	Motivation: Microarray gene expression data has increasingly become the common data source that can provide insights into biological processes at a system-wide level. One of the major problems with microarrays is that a dataset consists of relatively few time points with respect to a large number of genes, which makes the problem of inferring gene regulatory network an ill-posed one. On the other hand, gene expression data generated by different groups worldwide are increasingly accumulated on many species and can be accessed from public databases or individual websites, although each experiment has only a limited number of time-points. Results: This paper proposes a novel method to combine multiple time-course microarray datasets from different conditions for inferring gene regulatory networks. The proposed method is called GNR (Gene Network Reconstruction tool) which is based on linear programming and a decomposition procedure. The method theoretically ensures the derivation of the most consistent network structure with respect to all of the datasets, thereby not only significantly alleviating the problem of data scarcity but also remarkably improving the prediction reliability. We tested GNR using both simulated data and experimental data in yeast and Arabidopsis. The result demonstrates the effectiveness of GNR in terms of predicting new gene regulatory relationship in yeast and Arabidopsis.
DOI	10.1093/bioinformatics/btl396
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:000241271000014
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/3213
专题	应用数学研究所
通讯作者	Zhang, Xiang-Sun
作者单位	1.Osaka Sangyo Univ, Dept Elect Engn & Elect, Osaka 5748530, Japan 2.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China 3.Univ Missouri, Dept Comp Sci, Columbia, MO 65211 USA 4.Univ Missouri, Christopher S Bond Life Sci Ctr, Columbia, MO 65211 USA 5.Shanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
推荐引用方式 GB/T 7714	Wang, Yong,Joshi, Trupti,Zhang, Xiang-Sun,et al. Inferring gene regulatory networks from multiple microarray datasets[J]. BIOINFORMATICS,2006,22(19):2413-2420.
APA	Wang, Yong,Joshi, Trupti,Zhang, Xiang-Sun,Xu, Dong,&Chen, Luonan.(2006).Inferring gene regulatory networks from multiple microarray datasets.BIOINFORMATICS,22(19),2413-2420.
MLA	Wang, Yong,et al."Inferring gene regulatory networks from multiple microarray datasets".BIOINFORMATICS 22.19(2006):2413-2420.