NutriGenomeDB: a nutrigenomics exploratory and analytical platform

Authors: MARTIN-HERNANDEZ, ROBERTO - Imdea Institute; REGIERO, GUILLERMO - Autonomous University Of Madrid; ORDOVAS, JOSE - Jean Mayer Human Nutrition Research Center On Aging At Tufts University; DAVALOS, ALBERTO - Imdea Institute

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/1/2019
Publication Date: 10/28/2019
Citation: Martin-Hernandez, R., Regiero, G., Ordovas, J.M., Davalos, A. 2019. NutriGenomeDB: a nutrigenomics exploratory and analytical platform. Database: The Journal of Biological Databases and Curation. https://doi.org/10.1093/database/baz097.
DOI: https://doi.org/10.1093/database/baz097

Interpretive Summary: Habitual consumption of certain foods has been deemed beneficial or harmful against multiple chronic diseases. However, their classification in one or another category has changed over decades depending on the current evidence at the time. However, most of the evidence used for this purpose is epidemiological and cannot prove causality. In order to move the field forward towards a more precise and consistent risk assignment to foods, we need to understand their mechanisms of action. In this regard, many experiments have generated relevant and massive information that is available in public databases. Exploration of such data in an integrative manner offers excellent possibilities for gaining insights into the molecular effects of food compounds and bioactive molecules at the cellular level. Our objective was to create NutriGenomeDB, a web-based application that hosts manually curated gene sets defined from gene expression signatures, after differential expression analysis of nutrigenomics experiments performed on human cells. Through its web interface, users can explore gene expression data with interactive visualizations. We further demonstrate how the application can capture the primary molecular mechanisms of a drug used to treat hypertension and thus connect its mode of action with food compounds.

Technical Abstract: Habitual consumption of certain foods has shown beneficial and protective effects against multiple chronic diseases. However, it is not clear by which molecular mechanisms they may exert their beneficial effects. Multiple -omic experiments available in public databases have generated gene expression data following the treatment of human cells with different food nutrients and bioactive compounds. Exploration of such data in an integrative manner offers excellent possibilities for gaining insights into the molecular effects of food compounds and bioactive molecules at the cellular level. Here we present NutriGenomeDB, a web-based application that hosts manually curated gene sets defined from gene expression signatures, after differential expression analysis of nutrigenomics experiments performed on human cells available in the Gene Expression Omnibus (GEO) repository. Through its web interface, users can explore gene expression data with interactive visualizations. In addition, external gene signatures can be connected with nutrigenomics gene sets using a gene pattern-matching algorithm. We further demonstrate how the application can capture the primary molecular mechanisms of a drug used to treat hypertension and thus connect its mode of action with hosted food compounds.