Modeling mechanistic biological networks: An advanced Boolean approach

被引:15
|
作者
Handorf, T. [1 ]
Klipp, E. [1 ]
机构
[1] Univ Berlin, Dept Theoret Biophys, D-10115 Berlin, Germany
关键词
METABOLIC NETWORKS; SIGNAL-TRANSDUCTION; FUNCTIONAL-ANALYSIS; MATHEMATICAL-MODEL; PATHWAYS; DEFINITION; GLYCOLYSIS; DYNAMICS; SYSTEMS; YEAST;
D O I
10.1093/bioinformatics/btr697
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: The understanding of the molecular sources for diseases like cancer can be significantly improved by computational models. Recently, Boolean networks have become very popular for modeling signaling and regulatory networks. However, such models rely on a set of Boolean functions that are in general not known. Unfortunately, while detailed information on the molecular interactions becomes available in large scale through electronic databases, the information on the Boolean functions does not become available simultaneously and has to be included manually into the models, if at all known. Results: We propose a new Boolean approach which can directly utilize the mechanistic network information available through modern databases. The Boolean function is implicitly defined by the reaction mechanisms. Special care has been taken for the treatment of kinetic features like inhibition. The method has been applied to a signaling model combining the Wnt and MAPK pathway.
引用
收藏
页码:557 / 563
页数:7
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