MetaModule: a web tool to reconstruct, visualize and compare module-based metabolic networks

Metabolism is the set of chemical reactions that sustain life within organisms. They form a complex metabolic network, structured into smaller components called metabolic pathways, each dealing with a specific metabolic function. Pathways can be further divided into modules, which consist of a short chain of reactions that convert an initial compound into a target product. The organization of metabolic networks into pathways and modules is provided by the KEGG database, a reliable and widely known repository of metabolic data. In this thesis, we introduce a new module-based representation of metabolic networks called Module Graph. A Module Graph is a directed graph where nodes represent KEGG modules and edges describe the connectivity induced by common compounds. To explore the potential of Module Graphs we propose MetaModule, a web tool to reconstruct, visualize and compare metabolic networks represented as Module Graphs. MetaModule allows for reconstructing the Module Graph of a given species and for an interactive visualization of the resulting graph, enabling immediate visual inspection of modules and their connections. It also allows for comparing a pair of Module Graphs both visually and through specific similarity measures. MetaModule is equipped with an internal database to store useful metabolic information and provides APIs to expose the module-based graph reconstruction as a service. We use MetaModule to perform comparative analyses across different groups of organisms. The results indicate that Module Graphs offer a promising representation of metabolic networks, capable of distinguishing the various taxonomic groups of the considered species.