SynBioEcoli: a comprehensive metabolism network of engineered E. coli in three dimensional visualization

doi:10.1007/s40484-017-0098-1

Quantitative Biology

2017, Vol. 5

Issue (1): 99-104 https://doi.org/10.1007/s40484-017-0098-1

本期目录

SynBioEcoli: a comprehensive metabolism network of engineered E. coli in three dimensional visualization

Weizhong Tu², Shaozhen Ding¹, Ling Wu¹, Zhe Deng³, Hui Zhu³, Xiaotong Xu⁴, Chen Lin⁴, Chaonan Ye³, Minlu Han³, Mengna Zhao³, Juan Liu⁴, Zixin Deng³, Junni Chen², Dong-Qing Wei⁵, Qian-Nan Hu¹(

)

¹. Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
². Wuhan LifeSynther Cooperation Limited, Wuhan 430078, China
³. Ministry of Education, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
⁴. State Key Laboratory of Software Engineering and School of Computer Sciences, Wuhan University , Wuhan 430072, China
⁵. State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China

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Abstract：

Background: A comprehensive metabolism network of engineered E. coli is very important in systems biology and metabolomics studies. Many tools focus on two-dimensional space to display pathways in metabolic network. However, the usage of three-dimensional visualization may help to understand better the intricate topology of metabolic and regulatory networks.

Methods: We manually curated large amount of experimental data (including pathways, reactions and metabolites) from literature related with different types of engineered E. coli and then utilized a novel technology of three dimensional visualization to develop a comprehensive metabolic network named SynBioEcoli.

Results: SynBioEoli contains 740 biosynthetic pathways, 3,889 metabolic reactions, 2,255 chemical compoundsmanually curated from about 11,000 metabolism publications related with different types of engineered E. coli. Furthermore, SynBioEcoli integrates with various informatics techniques.

Conclusions: SynBioEcoli could be regarded as a comprehensive knowledgebase of engineered E. coli and represents the next generation cellular metabolism network visualization technology. It could be accessed via web browsers (such as Google Chrome) supporting WebGL, at http://www.rxnfinder.org/synbioecoli/.

Author Summary A comprehensive metabolism network of engineered E. coli is very important in systems biology and metabolomics studies. The usage of three-dimensional visualization may help to understand better metabolic and regulatory networks than many tools which focus on two-dimensional space. Based on the large amount of experimental data manually curated from publications related with different types of engineered E. coli and novel technology of three dimensional visualization, SynBioEcoli was developed, which also integrates with various informatics techniques. It could be regarded as a comprehensive knowledgebase of engineered E. coli and represents the next generation cellular metabolism network visualization technology.

Key words： engineered E. coli three dimensional metabolic network biosynthetic ability

收稿日期: 2016-09-09 出版日期: 2017-03-22

Corresponding Author(s): Qian-Nan Hu

引用本文:

. [J]. Quantitative Biology, 2017, 5(1): 99-104.
Weizhong Tu, Shaozhen Ding, Ling Wu, Zhe Deng, Hui Zhu, Xiaotong Xu, Chen Lin, Chaonan Ye, Minlu Han, Mengna Zhao, Juan Liu, Zixin Deng, Junni Chen, Dong-Qing Wei, Qian-Nan Hu. SynBioEcoli: a comprehensive metabolism network of engineered E. coli in three dimensional visualization. Quant. Biol., 2017, 5(1): 99-104.

链接本文:

https://academic.hep.com.cn/qb/CN/10.1007/s40484-017-0098-1
https://academic.hep.com.cn/qb/CN/Y2017/V5/I1/99

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