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ACS Chem Biol. 2019 Apr 19;14(4):704-714. doi: 10.1021/acschembio.8b01107. Epub 2019 Apr 4.

MAGI: A Method for Metabolite Annotation and Gene Integration.

Author information

1
Environmental Genomics and Systems Biology Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.
2
Data Analytics and Visualization Group, Computational Research Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.
3
Joint Genome Institute , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.
4
National Energy Research Scientific Computing Center , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.

Abstract

Metabolomics is a widely used technology for obtaining direct measures of metabolic activities from diverse biological systems. However, ambiguous metabolite identifications are a common challenge and biochemical interpretation is often limited by incomplete and inaccurate genome-based predictions of enzyme activities (that is, gene annotations). Metabolite Annotation and Gene Integration (MAGI) generates a metabolite-gene association score using a biochemical reaction network. This is calculated by a method that emphasizes consensus between metabolites and genes via biochemical reactions. To demonstrate the potential of this method, we applied MAGI to integrate sequence data and metabolomics data collected from Streptomyces coelicolor A3(2), an extensively characterized bacterium that produces diverse secondary metabolites. Our findings suggest that coupling metabolomics and genomics data by scoring consensus between the two increases the quality of both metabolite identifications and gene annotations in this organism. MAGI also made biochemical predictions for poorly annotated genes that were consistent with the extensive literature on this important organism. This limited analysis suggests that using metabolomics data has the potential to improve annotations in sequenced organisms and also provides testable hypotheses for specific biochemical functions. MAGI is freely available for academic use both as an online tool at https://magi.nersc.gov and with source code available at https://github.com/biorack/magi .

PMID:
30896917
DOI:
10.1021/acschembio.8b01107
[Indexed for MEDLINE]

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