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Comprehensive analysis of the mouse metabolome based on the transcriptome
Hidemasa Bono1, Itoshi Nikaido, Takeya Kasukawa
1Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Genome Research
|June 24, 2003
Summary
Researchers reconstructed the mouse metabolome using transcript sequences and pathway databases. This comprehensive analysis identified most known metabolic enzymes, revealing gaps in pathways like tryptophan metabolism for future research.
Area of Science:
- Mammalian biochemistry
- Transcriptomics
- Metabolomics
Background:
- The complete set of cDNAs for mammalian metabolic enzymes was previously unavailable.
- Understanding the full metabolic enzyme repertoire is crucial for systems biology.
Purpose of the Study:
- To reconstruct the mouse metabolome by identifying all encoding cDNAs.
- To establish a comprehensive catalog of mouse metabolic enzymes and their pathway associations.
Main Methods:
- Utilized the KEGG metabolic pathway database and Gene Ontology (GO) assignment.
- Integrated mouse representative transcript and protein set (RTPS), including FANTOM cDNA clones.
- Assigned Enzyme Commission (EC) numbers from GO molecular function ontology.
Main Results:
- Predicted 726 unique EC numbers for mouse metabolic enzymes, with 648 newly assigned.
- Confirmed representation of enzymes in major pathways like the tricarboxylic acid and urea cycles.
- Identified gaps in the tryptophan metabolism pathway, indicating missing enzyme cDNAs/genes.
Conclusions:
- The reconstructed mouse metabolome provides a near-complete enzymatic profile of known pathways.
- Coexpression data may help identify missing metabolic components and elucidate pathway connectivity.
- This resource offers new insights into mammalian metabolic pathway organization.