A linear programming model based on network flow for pathway inference

doi:10.1007/s11424-010-0206-z

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	A linear programming model based on network flow for pathway inference
	Ren, Xianwen; Zhang, Xiang-Sun
	2010-10-01
发表期刊	JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY
ISSN	1009-6124
卷号	23 期号:5 页码:971-977
摘要	Signal transduction pathways play important roles in various biological processes such as cell cycle, apoptosis, proliferation, differentiation and responses to the external stimuli. Efficient computational methods are of great demands to map signaling pathways systematically based on the interactome and microarray data in the post-genome era. This paper proposes a novel approach to infer the pathways based on the network flow well studied in the operation research. The authors define a potentiality variable for each protein to denote the extent to which it contributes to the objective pathway. And the capacity on each edge is not a constant but a function of the potentiality variables of the corresponding two proteins. The total potentiality of all proteins is given an upper bound. The approach is formulated to a linear programming model and solved by the simplex method. Experiments on the yeast sporulation data suggest this novel approach recreats successfully the backbone of the MAPK signaling pathway with a low upper bound of the total potentiality. By increasing the upper bound, the approach successfully predicts all the members of the Mitogen-activated protein kinases (MAPK) pathway responding to the pheromone. This simple but effective approach can also be used to infer the genetic information processing pathways underlying the expression quantitative trait loci (eQTL) associations, illustrated by the second example.
关键词	Gene expression linear programming network flow pathway inference protein interaction network
DOI	10.1007/s11424-010-0206-z
语种	英语
WOS研究方向	Mathematics
WOS类目	Mathematics, Interdisciplinary Applications
WOS记录号	WOS:000284074000010
出版者	SPRINGER HEIDELBERG
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/9659
专题	应用数学研究所
通讯作者	Ren, Xianwen
作者单位	Chinese Acad Sci, Inst Appl Math, Acad Math & Syst Sci, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Ren, Xianwen,Zhang, Xiang-Sun. A linear programming model based on network flow for pathway inference[J]. JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY,2010,23(5):971-977.
APA	Ren, Xianwen,&Zhang, Xiang-Sun.(2010).A linear programming model based on network flow for pathway inference.JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY,23(5),971-977.
MLA	Ren, Xianwen,et al."A linear programming model based on network flow for pathway inference".JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY 23.5(2010):971-977.