metabolite
Definition
A metabolite is a small molecule intermediate or end product of cellular metabolism, typically with a molecular weight under 1,500 Da. Metabolites include primary metabolites essential for growth and development (amino acids, nucleotides, sugars, lipids) and secondary metabolites involved in specialized functions (hormones, signaling molecules, pigments). They serve as substrates, products, or regulators in enzymatic reactions and biochemical pathways. Metabolites are key indicators of cellular state, reflecting the functional phenotype resulting from genetic, transcriptomic, and proteomic activities. Their analysis through metabolomics provides insights into disease mechanisms, drug responses, and metabolic disorders, making them crucial biomarkers in precision medicine and systems biology research.
Visualize metabolite in Nodes Bio
Researchers can visualize metabolite networks in Nodes Bio to map metabolic pathways, identify dysregulated metabolic nodes in disease states, and explore metabolite-enzyme-gene relationships. Network graphs reveal how metabolites cluster into functional modules, highlight rate-limiting steps, and show connections between different metabolic pathways. Users can integrate metabolomics data with transcriptomics and proteomics to understand multi-omics regulatory mechanisms and identify therapeutic targets.
Visualization Ideas:
- Metabolic pathway networks showing substrate-product relationships and enzyme catalysis
- Metabolite-protein interaction networks linking metabolites to their binding proteins and regulatory targets
- Multi-omics integration networks connecting metabolites to genes, transcripts, and proteins in disease contexts
Example Use Case
A cancer metabolism researcher investigates how tumor cells reprogram glucose metabolism. By mapping metabolite abundance data onto metabolic networks in Nodes Bio, they discover elevated lactate, reduced citrate, and accumulated glycolytic intermediates, confirming the Warburg effect. Network analysis reveals that specific metabolites like 2-hydroxyglutarate accumulate due to mutant IDH1 enzyme activity. The visualization shows downstream effects on histone methylation pathways, connecting metabolic alterations to epigenetic changes. This systems-level view identifies potential drug targets in the metabolic network that could selectively disrupt cancer cell metabolism.