HypeR-GEM: connecting metabolite signatures to enzyme-coding genes via genome-scale metabolic models.

ABSTRACT: Enrichment analysis is a cornerstone of "omics" data interpretation, enabling researchers to connect analysis results to biological processes and generate testable hypotheses. While well-established tools exist for transcriptomics and other omics layers, the development of robust enrichment resources for metabolomics remains comparatively limited. To address this gap, we developed hypeR-GEM, a methodology and associated R package that adapts gene set enrichment analysis to metabolomics. hypeR-GEM leverages genome-scale metabolic models (GEMs) to infer reaction-based links between metabolites and enzyme-coding genes, enabling the mapping of metabolite signatures to gene signatures and their subsequent annotation via gene set enrichment analysis. We validated hypeR-GEM u

SUBMITTER: Huang Z 

PROVIDER: S-EPMC12710827 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature