Further developments towards a genome-scale metabolic model of yeast.
Further developments towards a genome-scale metabolic model of yeast.
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DOI：
10.1186/1752-0509-4-145
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发表时间：
2010-10-28
影响因子：
--
通讯作者：
Mendes P
中科院分区：
文献类型：
--
作者：
Dobson PD;Smallbone K;Jameson D;Simeonidis E;Lanthaler K;Pir P;Lu C;Swainston N;Dunn WB;Fisher P;Hull D;Brown M;Oshota O;Stanford NJ;Kell DB;King RD;Oliver SG;Stevens RD;Mendes P
到目前为止，几个基因组规模的网络重建已被用于描述酵母酿酒酵母的代谢，每个在范围和内容上不同。最近的社区驱动的重建，而严格的证据和良好的注释，代表代谢物转运，脂质代谢和其他途径，并不服从约束为基础的分析，因为缺乏途径的连接。我们已经扩展了酵母网络重建，以纳入文献中的许多新反应，并以符合标准的方式表示这些反应。新的重建包括1102个独特的代谢反应，涉及924个独特的代谢物-在范围上明显大于任何以前的重建。特别是脂质代谢的代表性得到了改善，与脂质代谢相关的268种酶中有234种现在至少存在于一种反应中。连通性得到了显著改善，现在超过90%的代谢产物可从生长培养基成分中获得。目前的更新允许进行基于约束的分析;单敲除的可行性预测与体内实验的结果和以前的重建结果相当。我们报告了迄今为止最完整的酵母代谢重建的发展，该重建基于可靠的文献证据，并根据MIRIAM标准进行了丰富的注释。该重建可通过系统生物学标记语言（SBML）和可公开访问的数据库http://www.comp-sys-bio.org/yeastnet/获得。
To date, several genome-scale network reconstructions have been used to describe the metabolism of the yeast Saccharomyces cerevisiae, each differing in scope and content. The recent community-driven reconstruction, while rigorously evidenced and well annotated, under-represented metabolite transport, lipid metabolism and other pathways, and was not amenable to constraint-based analyses because of lack of pathway connectivity. We have expanded the yeast network reconstruction to incorporate many new reactions from the literature and represented these in a well-annotated and standards-compliant manner. The new reconstruction comprises 1102 unique metabolic reactions involving 924 unique metabolites - significantly larger in scope than any previous reconstruction. The representation of lipid metabolism in particular has improved, with 234 out of 268 enzymes linked to lipid metabolism now present in at least one reaction. Connectivity is emphatically improved, with more than 90% of metabolites now reachable from the growth medium constituents. The present updates allow constraint-based analyses to be performed; viability predictions of single knockouts are comparable to results from in vivo experiments and to those of previous reconstructions. We report the development of the most complete reconstruction of yeast metabolism to date that is based upon reliable literature evidence and richly annotated according to MIRIAM standards. The reconstruction is available in the Systems Biology Markup Language (SBML) and via a publicly accessible database http://www.comp-sys-bio.org/yeastnet/.
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影响因子：
46.9
作者：
Le Novère, N;Finney, A;Wanner, BL
通讯作者：
Wanner, BL
Miriam Resources：生成和解决系统生物学中强大的交叉引用的工具。
影响因子：
--
作者：
Laibe, Camille;Le Novere, Nicolas
通讯作者：
Le Novere, Nicolas
影响因子：
--
作者：
Mo ML;Palsson BO;Herrgård MJ
通讯作者：
Herrgård MJ
影响因子：
5.8
作者：
Bornstein, Benjamin J.;Keating, Sarah M.;Hucka, Michael
通讯作者：
Hucka, Michael
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J