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Browsing Metabolic and Regulatory Networks with BioCyc

Part of the Methods in Molecular Biology book series (MIMB,volume 804)

Abstract

The BioCyc database collection at BioCyc.org integrates genome and cellular network information for more than 1,100 organisms. This method chapter describes Web-based tools for browsing metabolic and regulatory networks within BioCyc. These tools allow visualization of complete metabolic and regulatory networks, and allow the user to zoom-in on regions of the network of interest. The user can find objects of interest such as genes and metabolites within the networks, and can selectively examine the connectivity of the network. The EcoCyc database within the BioCyc collection has been extensively curated. The descriptions within EcoCyc of the Escherichia coli metabolic network and regulatory network were derived from thousands of publications. Other BioCyc databases received moderate levels of curation, or no curation at all. Those databases receiving no curation contain metabolic networks that were computationally inferred from the annotated genome sequences of each organism.

Key words

  • Regulatory network
  • Metabolic network
  • Cellular network
  • Web interface
  • Highlighting
  • Regulatory subnetwork
  • Browsing
  • Genome database
  • Metabolic database

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References

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Acknowledgments

This work was supported by grant GM75742 from the National Institutes of Health. The contents of this chapter are solely the responsibility of the authors and do not necessarily represent the official views of the National Institutes of Health.

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Correspondence to Mario Latendresse .

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Latendresse, M., Paley, S., Karp, P.D. (2012). Browsing Metabolic and Regulatory Networks with BioCyc. In: van Helden, J., Toussaint, A., Thieffry, D. (eds) Bacterial Molecular Networks. Methods in Molecular Biology, vol 804. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-361-5_11

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  • DOI: https://doi.org/10.1007/978-1-61779-361-5_11

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  • Print ISBN: 978-1-61779-360-8

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