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
刊名	JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY
	2010-10-01
卷号	23 期号:5 页码:971-977
关键词	Gene expression linear programming network flow pathway inference protein interaction network
ISSN号	1009-6124
DOI	10.1007/s11424-010-0206-z
英文摘要	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.
WOS研究方向	Mathematics
语种	英语
出版者	SPRINGER HEIDELBERG
WOS记录号	WOS:000284074000010
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/9658]
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.