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| Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model |
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| Author(s): Duarte NC, Herrgard MJ, Palsson BO |
| Source: GENOME RESEARCH Volume: 14 Issue: 7 Pages: 1298-1309 Published: JUL 2004 |
| Times Cited: 151 References: 47 |
| Abstract: A fully compartmentalized genome-scale metabolic model of Saccharomyces cerevisiae that accounts for 750 genes and their associated transcripts, proteins, and reactions has been reconstructed and validated. All of the 1149 reactions included in this in silico model are both elementally and charge balanced and have been assigned to one of eight cellular locations (extracellular space, cytosol, mitochondrion, peroxisome, nucleus, endoplasmic reticulum, Golgi apparatus, or vacuole). When in silico predictions of 4154 growth phenotypes were compared to two published large-scale gene deletion studies, an 83% agreement was found between iND750's predictions and the experimental studies. Analysis of the failure modes showed that false predictions were primarily caused by iND750's limited inclusion of cellular processes outside of metabolism. This study systematically identified inconsistencies in our knowledge of yeast metabolism that require specific further experimental investigation. |
| Document Type: Article |
| Language: English |
| Reprint Address: Palsson, BO (reprint author), Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA |
Addresses:
1. Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA
2. Univ Calif San Diego, Bioinformat Grad Program, La Jolla, CA 92093 USA |
| Publisher: COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2924 USA |
| Subject Category: Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Genetics & Heredity |
| IDS Number: 834TQ |
| ISSN: 1088-9051 |
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