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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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 
54 and five different promoter types of the 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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  G. Li, B. Liu, and Y. Xu Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes Nucleic Acids Res., November 11, 2009; (2009) gkp907v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. J. Kersey, D. Lawson, E. Birney, P. S. Derwent, M. Haimel, J. Herrero, S. Keenan, A. Kerhornou, G. Koscielny, A. Kahari, et al. Ensembl genomes: Extending ensembl across the taxonomic space Nucleic Acids Res., November 1, 2009; (2009) gkp871v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. S. Novichkov, O. N. Laikova, E. S. Novichkova, M. S. Gelfand, A. P. Arkin, I. Dubchak, and D. A. Rodionov RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes Nucleic Acids Res., November 1, 2009; (2009) gkp894v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B.-M. Koo, V. A. Rhodius, G. Nonaka, P. L. deHaseth, and C. A. Gross Reduced capacity of alternative {sigma}s to melt promoters ensures stringent promoter recognition Genes & Dev., October 15, 2009; 23(20): 2426 - 2436. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Defrance and J. van Helden info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling Bioinformatics, October 15, 2009; 25(20): 2715 - 2722. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. J. Tree, D. Wang, C. McInally, A. Mahajan, A. Layton, I. Houghton, M. Elofsson, M. P. Stevens, D. L. Gally, and A. J. Roe Characterization of the Effects of Salicylidene Acylhydrazide Compounds on Type III Secretion in Escherichia coli O157:H7 Infect. Immun., October 1, 2009; 77(10): 4209 - 4220. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. N. Miller, L. R. Jarboe, P. C. Turner, P. Pharkya, L. P. Yomano, S. W. York, D. Nunn, K. T. Shanmugam, and L. O. Ingram Furfural Inhibits Growth by Limiting Sulfur Assimilation in Ethanologenic Escherichia coli Strain LY180 Appl. Envir. Microbiol., October 1, 2009; 75(19): 6132 - 6141. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Contreras-Moreira 3D-footprint: a database for the structural analysis of protein-DNA complexes Nucleic Acids Res., September 18, 2009; (2009) gkp781v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Sun, K. Lemmens, T. V. d. Bulcke, K. Engelen, B. D. Moor, and K. Marchal ViTraM: visualization of transcriptional modules Bioinformatics, September 15, 2009; 25(18): 2450 - 2451. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. A. F. T. van Hijum, M. H. Medema, and O. P. Kuipers Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation Microbiol. Mol. Biol. Rev., September 1, 2009; 73(3): 481 - 509. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Krawczyk, T. A. Kohl, A. Goesmann, J. Kalinowski, and J. Baumbach From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet Nucleic Acids Res., August 1, 2009; 37(14): e97 - e97. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Dingel and O. Milenkovic List-decoding methods for inferring polynomials in finite dynamical gene network models Bioinformatics, July 1, 2009; 25(13): 1686 - 1693. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Zhang, M. Xu, S. Li, and Z. Su Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes Nucleic Acids Res., June 1, 2009; 37(10): e72 - e72. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Marchais, M. Naville, C. Bohn, P. Bouloc, and D. Gautheret Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles Genome Res., June 1, 2009; 19(6): 1084 - 1092. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. D. Passalacqua, A. Varadarajan, B. D. Ondov, D. T. Okou, M. E. Zwick, and N. H. Bergman Structure and Complexity of a Bacterial Transcriptome J. Bacteriol., May 15, 2009; 191(10): 3203 - 3211. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. C. Malinverni and T. J. Silhavy An ABC transport system that maintains lipid asymmetry in the Gram-negative outer membrane PNAS, May 12, 2009; 106(19): 8009 - 8014. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. C. Pulvermacher, L. T. Stauffer, and G. V. Stauffer Role of the sRNA GcvB in regulation of cycA in Escherichia coli Microbiology, January 1, 2009; 155(1): 106 - 114. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Collado-Vides, H. Salgado, E. Morett, S. Gama-Castro, V. Jimenez-Jacinto, I. Martinez-Flores, A. Medina-Rivera, L. Muniz-Rascado, M. Peralta-Gil, and A. Santos-Zavaleta Bioinformatics Resources for the Study of Gene Regulation in Bacteria J. Bacteriol., January 1, 2009; 191(1): 23 - 31. [Full Text] [PDF]
|
|
|
|
 |
|
 J. Baumbach, A. Tauch, and S. Rahmann Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks Brief Bioinform, January 1, 2009; 10(1): 75 - 83. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Grote, J. Klein, I. Retter, I. Haddad, S. Behling, B. Bunk, I. Biegler, S. Yarmolinetz, D. Jahn, and R. Munch PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes Nucleic Acids Res., January 1, 2009; 37(suppl_1): D61 - D65. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Pertea, K. Ayanbule, M. Smedinghoff, and S. L. Salzberg OperonDB: a comprehensive database of predicted operons in microbial genomes Nucleic Acids Res., January 1, 2009; 37(suppl_1): D479 - D482. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. M. Keseler, C. Bonavides-Martinez, J. Collado-Vides, S. Gama-Castro, R. P. Gunsalus, D. A. Johnson, M. Krummenacker, L. M. Nolan, S. Paley, I. T. Paulsen, et al. EcoCyc: A comprehensive view of Escherichia coli biology Nucleic Acids Res., January 1, 2009; 37(suppl_1): D464 - D470. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Mao, P. Dam, J. Chou, V. Olman, and Y. Xu DOOR: a database for prokaryotic operons Nucleic Acids Res., January 1, 2009; 37(suppl_1): D459 - D463. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-Y. Huang, H.-Y. Chang, C.-H. Chou, C.-P. Tseng, S.-Y. Ho, C.-D. Yang, Y.-W. Ju, and H.-D. Huang sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes Nucleic Acids Res., January 1, 2009; 37(suppl_1): D150 - D154. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Klein, S. Leupold, R. Munch, C. Pommerenke, T. Johl, U. Karst, L. Jansch, D. Jahn, and I. Retter ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks Nucleic Acids Res., July 1, 2008; 36(suppl_2): W460 - W464. [Abstract] [Full Text] [PDF]
|
|