Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network.
Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network.
复制标题
DOI：
10.1186/1752-0509-6-55
复制
发表时间：
2012-06-04
影响因子：
--
通讯作者：
Walker LP
中科院分区：
文献类型：
--
作者：
Heavner BD;Smallbone K;Barker B;Mendes P;Walker LP
自从2003年发表了第一个化学计量约束的酵母基因组规模代谢模型以来，一直在努力改进酿酒酵母生化反应网络的计算重建和改进可以从这种重建中得到的化学计量约束的代谢模型。继续这个正在进行的过程，我们构建了酵母共识重建的更新，酵母5。酵母共识重建是努力建立基于社区的重建的产物，强调通过基于证据的反应选择的标准合规性和生化准确性。它利用了各种独立研究小组发表的模型以及从生物化学数据库和主要文献中获得的信息。酵母5细化了重建中包含的生化反应，特别是涉及鞘脂代谢的反应;更新了基因反应注释;并强调了重建和化学计量约束模型之间的区别。虽然这不是主要目标，但这一更新也提高了模型预测活力和营养缺陷型表型的准确性，并增加了上位相互作用的数量。本次更新强调标准合规性、明确的代谢物命名以及通过结构化文件格式提供的计算机可读注释。此外，我们还开发了MATLAB脚本来评估模型的预测准确性，并演示基本的模型应用程序，例如模拟有氧和厌氧生长。这些脚本为使用通量平衡分析评估各种化学计量约束的酵母代谢模型的性能提供了独立的工具，作为附加文件1，2和3包括在内。Yeast 5扩展和改进了酵母代谢的计算重建，并提高了化学计量约束酵母代谢模型的预测准确性。它与以前的重建和模型的不同之处在于强调了酵母代谢重建和化学计量约束模型之间的区别，并且作为附加文件4和附加文件5以及在http://yeast.sf.net/上作为单独的系统生物学标记语言（SBML）文件提供。通过这种分离，我们打算使建模过程更容易访问，更明确，更透明，更可重复。
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. 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. Yeast 5 expands and refines the computational reconstruction of yeast metabolism and improves the predictive accuracy of a stoichiometrically constrained yeast metabolic model. It differs from previous reconstructions and models by emphasizing the distinction between the yeast metabolic reconstruction and the stoichiometrically constrained model, and makes both available as Additional file 4 and Additional file 5 and at http://yeast.sf.net/ as separate systems biology markup language (SBML) files. Through this separation, we intend to make the modeling process more accessible, explicit, transparent, and reproducible.
登录
查看更多内容
DOI：
10.1038/nrmicro1949
发表时间：
2009-02
期刊：
Nature reviews. Microbiology
影响因子：
--
作者：
通讯作者：
--
影响因子：
--
作者：
Mo ML;Palsson BO;Herrgård MJ
通讯作者：
Herrgård MJ
影响因子：
12.3
作者：
Blank LM;Kuepfer L;Sauer U
通讯作者：
Sauer U
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J
影响因子：
3.7
作者：
Aho, Tommi;Almusa, Henrikki;Yli-Harja, Olli
通讯作者：
Yli-Harja, Olli