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Extracting Regulatory Networks of Escherichia coli from RegulonDB

  • Heladia Salgado
  • Irma Martínez-Flores
  • Alejandra López-Fuentes
  • Jair Santiago García-Sotelo
  • Liliana Porrón-Sotelo
  • Hilda Solano
  • Luis Muñiz-Rascado
  • Julio Collado-Vides
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 804)

Abstract

RegulonDB contains the largest and currently best-known data set on transcriptional regulation in a single free-living organism, that of Escherichia coli K-12 (Gama-Castro et al. Nucleic Acids Res 36:D120–D124, 2008). This organized knowledge has been the gold standard for the implementation of bioinformatic predictive methods on gene regulation in bacteria (Collado-Vides et al. J Bacteriol 191:23–31, 2009). Given the complexity of different types of interactions, the difficulty of visualizing in a single figure of the whole network, and the different uses of this knowledge, we are making available different views of the genetic network. This chapter describes case studies about how to access these views, via precomputed files, web services and SQL, including sigma–gene relationships corresponding to transcription of alternative RNA polymerase holoenzyme promoters; as well as, transcription factor (TF)-genes, TF–operons, TF–TF, and TF–regulon interactions. 17

Key words

Bacterial Regulatory networks RegulonDB Escherichia coli Transcription factor Gene Operon Sigma factor Regulatory interactions Database Web services 

Notes

Acknowledgments

We acknowledge the technical support of Shirley Alquicira and Víctor del Moral Chávez.

This work was funded by the National Institutes of Health, grant numbers R01 GM071962-05 and by UNAM, PAPIIT grant number IN214905. We acknowledge support from CONACYT PROINNOVA-2010 project number 134817.

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Heladia Salgado
    • 1
  • Irma Martínez-Flores
    • 1
  • Alejandra López-Fuentes
    • 1
  • Jair Santiago García-Sotelo
    • 1
  • Liliana Porrón-Sotelo
    • 1
  • Hilda Solano
    • 1
  • Luis Muñiz-Rascado
    • 1
  • Julio Collado-Vides
    • 1
  1. 1.Programa de Genómica Computacional, Centro de Ciencias GenómicasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico

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