Comparative study of computational methods to detect the correlated reaction sets in biochemical networks

Correlated reaction sets (Co-Sets) are mathematically defined modules in biochemical reaction networks which facilitate the study of biological processes by decomposing complex reaction networks into conceptually simple units. According to the degree of association, Co-Sets can be classified into three types: perfect, partial and directional. Five approaches have been developed to calculate Co-Sets, including network-based pathway analysis, Monte Carlo sampling, linear optimization, enzyme subsets and hard-coupled reaction sets. However, differences in design and implementation of these methods lead to discrepancies in the resulted Co-Sets as well as in their use in biotechnology which need careful interpretation. In this paper, we provide a comparative study of the methods for Co-Sets computing in detail from four aspects: (i) sensitivity, (ii) completeness and soundness, (iii) flexibility and (iv) scalability. By applying them to Escherichia coli core metabolic network, the differences and relationships among these methods are clearly articulated which may be useful for potential users.