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Quantitative Biology

, Volume 5, Issue 1, pp 99–104 | Cite as

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

  • 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
Research Article
  • 163 Downloads

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 compounds manually 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/.

Keywords

engineered E. coli three dimensional metabolic network biosynthetic ability 

Notes

Acknowledgements

This work was supported by the National Science Foundation of China (Nos. 31270101 and 31570092), the National High Technology Research and Development Program (No. 2012CB721000) and the Natural Science Foundation of Tianjin, China.

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Copyright information

© Higher Education Press and Springer-Verlag GmbH 2017

Authors and Affiliations

  • Weizhong Tu
    • 2
  • Shaozhen Ding
    • 1
  • Ling Wu
    • 1
  • Zhe Deng
    • 3
  • Hui Zhu
    • 3
  • Xiaotong Xu
    • 4
  • Chen Lin
    • 4
  • Chaonan Ye
    • 3
  • Minlu Han
    • 3
  • Mengna Zhao
    • 3
  • Juan Liu
    • 4
  • Zixin Deng
    • 3
  • Junni Chen
    • 2
  • Dong-Qing Wei
    • 5
  • Qian-Nan Hu
    • 1
  1. 1.Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
  2. 2.Wuhan LifeSynther Cooperation LimitedWuhanChina
  3. 3.Ministry of Education, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery and School of Pharmaceutical SciencesWuhan UniversityWuhanChina
  4. 4.State Key Laboratory of Software Engineering and School of Computer SciencesWuhan UniversityWuhanChina
  5. 5.State Key Laboratory of Microbial MetabolismShanghai Jiao Tong UniversityShanghaiChina

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