Related Experiment Video
Updated: Jun 2, 2026

CorrelationCalculator and Filigree: Tools for Data-Driven Network Analysis of Metabolomics Data
Published on: November 10, 2023
A survey of metabolic databases emphasizing the MetaCyc family
1Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA, 94025, USA. pkarp@ai.sri.com
Abstract:
Thanks to the confluence of genome sequencing and bioinformatics, the number of metabolic databases has expanded from a handful in the mid-1990s to several thousand today. These databases lie within distinct families that have common ancestry and common attributes. The main families are the MetaCyc, KEGG, Reactome, Model SEED, and BiGG families. We survey these database families, as well as important individual metabolic databases, including multiple human metabolic databases. The MetaCyc family is described in particular detail. It contains well over 1,000 databases, including highly curated databases for Escherichia coli, Saccharomyces cerevisiae, Mus musculus, and Arabidopsis thaliana. These databases are available through a number of web sites that offer a range of software tools for querying and visualizing metabolic networks. These web sites also provide multiple tools for analysis of gene expression and metabolomics data, including visualization of those datasets on metabolic network diagrams and over-representation analysis of gene sets and metabolite sets.
Related Concept Videos
Overview of Metabolism
Plant Metabolism
Sunlight, the primary source of energy in plants, is first absorbed by the chlorophyll pigments present in their leaves. Plants then use this energy to carry out photosynthesis, where water is oxidized into oxygen and carbon dioxide...
Metabolism of Chemolithotrophs
Overview of Protein Metabolism
Amino acids play various roles in the body once they are absorbed into cells. They are restructured...
Overview of Fatty Acid Metabolism
Fatty acids are catabolized in a process called beta-oxidation, which takes place in the matrix of the mitochondria and converts their fatty acid chains into two-carbon units of acetyl groups. The acetyl...
Introduction to Metabolism
Regulation of Metabolism

