Pathway analysis

Metabolic pathways are the foundation for understanding metabolomic data in its biochemical context. By mapping metabolomic results to these pathways and identifying those which are altered in the experiment, we can easily add biological interpretability to our experimental results. However, to perform these analyses in a robust, reproducible way, we first need to describe the measured metabolites in a standardized manner; hence, we begin this chapter by examining ontologies. We then proceed to shortly review the pathway databases available for metabolomic data. We explain the range of methods applied for these analyzes, examining their key differences and focusing on the potential sources of bias in the results from each and we conclude with a section about the tools available for metabolomic pathway analysis.