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Open Access Research article

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

Xianwen Ren1, Xiaobo Zhou2, Ling-Yun Wu1 and Xiang-Sun Zhang1*

Author Affiliations

1 Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China

2 Center for Biotechnology and Informatics, The Methodist Hospital Research Institute and Department of Radiology, The Methodist Hospital, Weill Cornell Medical College, Houston, TX 77030, USA

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BMC Systems Biology 2010, 4:72  doi:10.1186/1752-0509-4-72

Published: 27 May 2010

Abstract

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.