SUMMER, a shiny utility for metabolomics and multiomics exploratory research

INTRODUCTION: Cellular metabolites are generated by a complex network of biochemical reactions. This makes interpreting changes in metabolites exceptionally challenging. OBJECTIVES: To develop a computational tool that integrates multiomics data at the level of reactions. METHODS: Changes in metabolic reactions are modeled with input from transcriptomics/proteomics measurements of enzymes and metabolomic measurements of metabolites. RESULTS: We developed SUMMER, which identified more relevant signals, key metabolic reactions, and relevant underlying biological pathways in a real-world case study. CONCLUSION: SUMMER performs integrative analysis for data interpretation and exploration. SUMMER is freely accessible at http://summer.salk.edu and the code is available at https://bitbucket.org/salkigc/summer. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11306-020-01750-7) contains supplementary material, which is available to authorized users.