This Article Full Text Full Text (PDF) Supplemental Research Data Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Gutiérrez-Ríos, R. M. Articles by Collado-Vides, J. Search for Related Content PubMed PubMed Citation Articles by Gutiérrez-Ríos, R. M. Articles by Collado-Vides, J. Social Bookmarking                   What's this?

Letter

Regulatory Network of Escherichia coli: Consistency Between Literature Knowledge and Microarray Profiles

¹ Program of Computational Genomics, Centro de Investigación sobre Fijación de Nitrógeno, Univercidad Nacional Autónoma de México (CIFN-UNAM), Morelos 62100, México ² Genome Center, University of Wisconsin, Madison, Wisconsin 53706, USA ³ Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, UNAM, 01000 México D. F., México

The transcriptional network of Escherichia coli may well be the most complete experimentally characterized network of a single cell. A rule-based approach was built to assess the degree of consistency between whole-genome microarray experiments in different experimental conditions and the accumulated knowledge in the literature compiled in RegulonDB, a data base of transcriptional regulation and operon organization in E. coli. We observed a high and statistical significant level of consistency, ranging from 70%-87%. When effector metabolites of regulatory proteins are not considered in the prediction of the active or inactive state of the regulators, consistency falls by up to 40%. Similarly, consistency decreases when rules for multiple regulatory interactions are altered or when "on" and "off" entries were assigned randomly. We modified the initial state of regulators and evaluated the propagation of errors in the network that do not correlate linearly with the connectivity of regulators. We interpret this deviation mainly as a result of the existence of redundant regulatory interactions. Consistency evaluation opens a new space of dialogue between theory and experiment, as the consequences of different assumptions can be evaluated and compared.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1387003.

[Supplemental material is available online at www.genome.org. The data set and supplemental material are available at http://www.cifn.unam.mx/Computational_Genomics/Consistency/.]

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				S. Gama-Castro, V. Jimenez-Jacinto, M. Peralta-Gil, A. Santos-Zavaleta, M. I. Penaloza-Spinola, B. Contreras-Moreira, J. Segura-Salazar, L. Muniz-Rascado, I. Martinez-Flores, H. Salgado, et al. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation Nucleic Acids Res., January 11, 2008; 36(suppl_1): D120 - D124. [Abstract] [Full Text] [PDF]

				S. C. Janga, H. Salgado, A. Martinez-Antonio, and J. Collado-Vides Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli Nucleic Acids Res., November 29, 2007; 35(20): 6963 - 6972. [Abstract] [Full Text] [PDF]

				S. R. Chhabra, Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T. C. Hazen, J. D. Wall, J. Zhou, et al. Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough. J. Bacteriol., March 1, 2006; 188(5): 1817 - 1828. [Abstract] [Full Text] [PDF]

				I. Zwir, H. Huang, and E. A. Groisman Analysis of differentially-regulated genes within a regulatory network by GPS genome navigation Bioinformatics, November 15, 2005; 21(22): 4073 - 4083. [Abstract] [Full Text] [PDF]

				S. Herold, J. Siebert, A. Huber, and H. Schmidt Global Expression of Prophage Genes in Escherichia coli O157:H7 Strain EDL933 in Response to Norfloxacin Antimicrob. Agents Chemother., March 1, 2005; 49(3): 931 - 944. [Abstract] [Full Text] [PDF]

				Z. Zhang, G. Gosset, R. Barabote, C. S. Gonzalez, W. A. Cuevas, and M. H. Saier Jr. Functional Interactions between the Carbon and Iron Utilization Regulators, Crp and Fur, in Escherichia coli J. Bacteriol., February 1, 2005; 187(3): 980 - 990. [Abstract] [Full Text] [PDF]

				H.-W. Ma, B. Kumar, U. Ditges, F. Gunzer, J. Buer, and A.-P. Zeng An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs Nucleic Acids Res., December 16, 2004; 32(22): 6643 - 6649. [Abstract] [Full Text] [PDF]

				H. Salgado, S. Gama-Castro, A. Martinez-Antonio, E. Diaz-Peredo, F. Sanchez-Solano, M. Peralta-Gil, D. Garcia-Alonso, V. Jimenez-Jacinto, A. Santos-Zavaleta, C. Bonavides-Martinez, et al. RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12 Nucleic Acids Res., January 1, 2004; 32(90001): D303 - 306. [Abstract] [Full Text] [PDF]