An information-flow-based model with dissipation, saturation and direction for active pathway inference

doi:10.1186/1752-0509-4-72

CSpace > 应用数学研究所

	An information-flow-based model with dissipation, saturation and direction for active pathway inference
	Ren, Xianwen 1; Zhou, Xiaobo 2,3; Wu, Ling-Yun1 ; Zhang, Xiang-Sun1
	2010-05-27
发表期刊	BMC SYSTEMS BIOLOGY
ISSN	1752-0509
卷号	4 页码:10
摘要	Background: Biological systems process the genetic information and environmental signals through pathways. How to map the pathways systematically and efficiently from high-throughput genomic and proteomic data is a challenging open problem. Previous methods design different heuristics but do not describe explicitly the behaviours of the information flow. Results: In this study, we propose new concepts of dissipation, saturation and direction to decipher the information flow behaviours in the pathways and thereby infer the biological pathways from a given source to its target. This model takes into account explicitly the common features of the information transmission and provides a general framework to model the biological pathways. It can incorporate different types of bio-molecular interactions to infer the signal transduction pathways and interpret the expression quantitative trait loci (eQTL) associations. The model is formulated as a linear programming problem and thus is solved efficiently. Experiments on the real data of yeast indicate that the reproduced pathways are highly consistent with the current knowledge. Conclusions: Our model explicitly treats the biological pathways as information flows with dissipation, saturation and direction. The effective applications suggest that the three new concepts may be valid to describe the organization rules of biological pathways. The deduced linear programming should be a promising tool to infer the various biological pathways from the high-throughput data.
DOI	10.1186/1752-0509-4-72
语种	英语
资助项目	NIH[R01 LM010185-01] ; Chinese NSFC[60873205] ; Chinese NSFC[2006CB503905]
WOS研究方向	Mathematical & Computational Biology
WOS类目	Mathematical & Computational Biology
WOS记录号	WOS:000279942900001
出版者	BIOMED CENTRAL LTD
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/218
专题	应用数学研究所
通讯作者	Zhang, Xiang-Sun
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 2.Methodist Hosp, Res Inst, Ctr Biotechnol & Informat, Houston, TX 77030 USA 3.Methodist Hosp, Weill Cornell Med Coll, Dept Radiol, Houston, TX 77030 USA
推荐引用方式 GB/T 7714	Ren, Xianwen,Zhou, Xiaobo,Wu, Ling-Yun,et al. An information-flow-based model with dissipation, saturation and direction for active pathway inference[J]. BMC SYSTEMS BIOLOGY,2010,4:10.
APA	Ren, Xianwen,Zhou, Xiaobo,Wu, Ling-Yun,&Zhang, Xiang-Sun.(2010).An information-flow-based model with dissipation, saturation and direction for active pathway inference.BMC SYSTEMS BIOLOGY,4,10.
MLA	Ren, Xianwen,et al."An information-flow-based model with dissipation, saturation and direction for active pathway inference".BMC SYSTEMS BIOLOGY 4(2010):10.