Crosstalk between Metabolic and Regulatory Pathways

Abstract

To enhance the understanding of cells’ response in a specific condition, one requires information that shows the interconnected view of biological process. Broadly speaking, biological pathways fall into two functional categories: metabolic and regulatory pathways. Existing pathway databases are categorizing specific pathway types according to their own definition about their own subject. They contain protein and/or interaction data through clickable image pathway maps. Currently, the crosstalk among different pathways is restricted in metabolic pathways. Metabolic pathway information has a hierarchical structure as we can see in KEGG [3]. In the finest resolution, entities are compounds and reactions between them. In the upper level, a pathway itself will be a node and the interconnected nature of cells’ metabolism is represented as edges. Therefore, metabolisms are represented as many layers of different elements in their hierarchy. However, the available information of the regulatory pathway has neither a hierarchical concept nor a whole proteome scale view of crosstalk between the pathways. As a result, we have trouble to understand interconnection between metabolic and regulatory pathways because of the inherent difference of two kinds of pathways. For this reason, we integrated different kinds of pathway database: KEGG/BIND and protein information supplement database SWISS-PROT [1, 2]. In this paper, we describe several issues for database construction and crosstalk between different kinds of pathways. Because these kinds of pathways are interconnected for the same stimuli, the integrated understanding of all kinds of pathway will be a framework for the systems biology.