期刊论文

【摘要】

Background

Efforts to improve the computational reconstruction of the Saccharomyces cerevisiae biochemical reaction network and to refine the stoichiometrically constrained metabolic models that can be derived from such a reconstruction have continued since the first stoichiometrically constrained yeast genome scale metabolic model was published in 2003. Continuing this ongoing process, we have constructed an update to the Yeast Consensus Reconstruction, Yeast 5. The Yeast Consensus Reconstruction is a product of efforts to forge a community-based reconstruction emphasizing standards compliance and biochemical accuracy via evidence-based selection of reactions. It draws upon models published by a variety of independent research groups as well as information obtained from biochemical databases and primary literature.

Results

Yeast 5 refines the biochemical reactions included in the reconstruction, particularly reactions involved in sphingolipid metabolism; updates gene-reaction annotations; and emphasizes the distinction between reconstruction and stoichiometrically constrained model. Although it was not a primary goal, this update also improves the accuracy of model prediction of viability and auxotrophy phenotypes and increases the number of epistatic interactions. This update maintains an emphasis on standards compliance, unambiguous metabolite naming, and computer-readable annotations available through a structured document format. Additionally, we have developed MATLAB scripts to evaluate the model’s predictive accuracy and to demonstrate basic model applications such as simulating aerobic and anaerobic growth. These scripts, which provide an independent tool for evaluating the performance of various stoichiometrically constrained yeast metabolic models using flux balance analysis, are included as Additional files 1, 2 and 3.

Additional file 1. Function testYeastModel.m.m.

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【授权许可】

2012 Heavner et al.; licensee BioMed Central Ltd.

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Figure 1.

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BMC Systems Biology
Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

Larry P Walker² Pedro Mendes⁴ Brandon Barker¹ Kieran Smallbone³ Benjamin D Heavner²
[1] Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA;Department of Biological & Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA;Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, M1 7DN, UK;School of Computer Science, University of Manchester, Manchester, M13 9PL, UK
关键词: Model; GENRE; GEM; Flux balance analysis; Yeast; Reconstruction; Metabolic;
Others : 1144347 DOI : 10.1186/1752-0509-6-55

received in 2012-03-02, accepted in 2012-06-04, 发布年份 2012
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【 摘 要 】

Background

Results

【 授权许可】

【 预 览 】

【 图 表 】

【 参考文献 】

【摘要】

【授权许可】

【预览】

【图表】

【参考文献】