Integrated visualization of metabolomics and transcriptomics with Galaxy

The regulation of cell metabolism is complex and multifold. Hence the metabolic alterations that have been reported in many physio-pathological conditions can be fully charac- terized only by using model-based multi-omics data integration frameworks. We present here version 2 of the Marea4Galaxy tool, integrated into the Galaxy platform. The previous version of Marea4Galaxy allowed users to visualize deregulated reactions at the transcriptomic level. The new version extends these capabilities by enabling the simultaneous visualization of dereg- ulated reactions at the metabolic level using metabolomics data. Significant improvements have been made, including a more comprehensive metabolic network model, a module for extract- ing necessary inputs from any metabolic model in XML or JSON format, better compatibility with alternative gene nomenclatures, and faster reaction activity scores (RASs) calculation. We demonstrate the utility of this tool by comparing different groups of cancer cell lines using paired datasets from the Cancer Cell Line Encyclopedia.