An information-flow-based model with dissipation, saturation and direction for active pathway inference.
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.
Ren
Xianwen
X
Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China.
Zhou
Xiaobo
X
Wu
Ling-Yun
LY
Zhang
Xiang-Sun
XS
D053263:Gene Regulatory Networks / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D007254:Information Science; D020928:Mitogen-Activated Protein Kinases / Q000378:metabolism; D008954:Models, Biological; D011382:Programming, Linear; D020543:Proteome / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics*; D015003:Yeasts
D020543:Proteome; D020928:Mitogen-Activated Protein Kinases