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Nucleic Acids Research Advance Access originally published online on December 23, 2007
Nucleic Acids Research 2008 36(Database issue):D120-D124; doi:10.1093/nar/gkm994
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Nucleic Acids Research, 2008, Vol. 36, Database issue D120-D124
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation

Socorro Gama-Castro1, Verónica Jiménez-Jacinto1, Martín Peralta-Gil1, Alberto Santos-Zavaleta1, Mónica I. Peñaloza-Spinola1, Bruno Contreras-Moreira1, Juan Segura-Salazar1, Luis Muñiz-Rascado1, Irma Martínez-Flores1, Heladia Salgado1, César Bonavides-Martínez1, Cei Abreu-Goodger1, Carlos Rodríguez-Penagos1, Juan Miranda-Ríos2, Enrique Morett2, Enrique Merino2, Araceli M. Huerta1, Luis Treviño-Quintanilla1 and Julio Collado-Vides1,*

1Program of Computational Genomics, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico and 2Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3, Cuernavaca, Morelos 62100, Mexico

*To whom correspondence should be addressed. Tel: +52 (777) 3139877; Fax: +52 (777) 3175581; Email: ecoli-t1{at}ccg.unam.mx

Received September 14, 2007. Revised October 19, 2007. Accepted October 22, 2007.

RegulonDB (http://regulondb.ccg.unam.mx/) is the primary reference database offering curated knowledge of the transcriptional regulatory network of Escherichia coli K12, currently the best-known electronically encoded database of the genetic regulatory network of any free-living organism. This paper summarizes the improvements, new biology and new features available in version 6.0. Curation of original literature is, from now on, up to date for every new release. All the objects are supported by their corresponding evidences, now classified as strong or weak. Transcription factors are classified by origin of their effectors and by gene ontology class. We have now computational predictions for {sigma}54 and five different promoter types of the {sigma}70 family, as well as their corresponding –10 and –35 boxes. In addition to those curated from the literature, we added about 300 experimentally mapped promoters coming from our own high-throughput mapping efforts. RegulonDB v.6.0 now expands beyond transcription initiation, including RNA regulatory elements, specifically riboswitches, attenuators and small RNAs, with their known associated targets. The data can be accessed through overviews of correlations about gene regulation. RegulonDB associated original literature, together with more than 4000 curation notes, can now be searched with the Textpresso text mining engine.


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