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Heladia Salgado,
Martin Peralta-Gil,
Socorro Gama-Castro,
Alberto Santos-Zavaleta, Luis Muñiz-Rascado,
Jair S García-Sotelo,
Verena Weiss,
Hilda Solano-Lira,
Irma Martínez-Flores,
Alejandra Medina-Rivera, [......],
Yalbi I Balderas-Martínez,
Lucia Pannier,
Maricela Olvera,
Aurora Labastida,
Verónica Jiménez-Jacinto,
Leticia Vega-Alvarado,
Victor Del Moral-Chávez,
Alfredo Hernández-Alvarez,
Enrique Morett,
Julio Collado-Vides
[show abstract]
[hide abstract]
ABSTRACT: This article summarizes our progress with RegulonDB (http://regulondb.ccg.unam.mx/) during the past 2 years. We have kept up-to-date the knowledge from the published literature regarding transcriptional regulation in Escherichia coli K-12. We have maintained and expanded our curation efforts to improve the breadth and quality of the encoded experimental knowledge, and we have implemented criteria for the quality of our computational predictions. Regulatory phrases now provide high-level descriptions of regulatory regions. We expanded the assignment of quality to various sources of evidence, particularly for knowledge generated through high-throughput (HT) technology. Based on our analysis of most relevant methods, we defined rules for determining the quality of evidence when multiple independent sources support an entry. With this latest release of RegulonDB, we present a new highly reliable larger collection of transcription start sites, a result of our experimental HT genome-wide efforts. These improvements, together with several novel enhancements (the tracks display, uploading format and curational guidelines), address the challenges of incorporating HT-generated knowledge into RegulonDB. Information on the evolutionary conservation of regulatory elements is also available now. Altogether, RegulonDB version 8.0 is a much better home for integrating knowledge on gene regulation from the sources of information currently available.
Nucleic Acids Research 11/2012; · 8.03 Impact Factor
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Ingrid M Keseler,
Amanda Mackie,
Martin Peralta-Gil,
Alberto Santos-Zavaleta,
Socorro Gama-Castro,
César Bonavides-Martínez,
Carol Fulcher,
Araceli M Huerta,
Anamika Kothari,
Markus Krummenacker, [......],
Imke Schröder,
Alexander G Shearer,
Pallavi Subhraveti,
Mike Travers,
Deepika Weerasinghe,
Verena Weiss,
Julio Collado-Vides,
Robert P Gunsalus,
Ian Paulsen,
Peter D Karp
[show abstract]
[hide abstract]
ABSTRACT: EcoCyc (http://EcoCyc.org) is a model organism database built on the genome sequence of Escherichia coli K-12 MG1655. Expert manual curation of the functions of individual E. coli gene products in EcoCyc has been based on information found in the experimental literature for E. coli K-12-derived strains. Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc.
Nucleic Acids Research 11/2012; · 8.03 Impact Factor
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[show abstract]
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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.
Methods in molecular biology (Clifton, N.J.) 01/2012; 804:179-95.
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Socorro Gama-Castro,
Heladia Salgado,
Martín Peralta-Gil,
Alberto Santos-Zavaleta, Luis Muñiz-Rascado,
Hilda Solano-Lira,
Verónica Jiménez-Jacinto,
Verena Weiss,
Jair S. García-Sotelo,
Alejandra López-Fuentes, [......],
Araceli M. Huerta,
Alfredo Mendoza-Vargas,
Leonardo Collado-Torres,
Blanca Taboada,
Leticia Vega-Alvarado,
Maricela Olvera,
Leticia Olvera,
Ricardo Grande,
Enrique Morett,
Julio Collado-Vides
Nucleic Acids Research. 01/2011; 39:98-105.
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Ingrid M. Keseler,
Julio Collado-Vides,
Alberto Santos-Zavaleta,
Martín Peralta-Gil,
Socorro Gama-Castro, Luis Muñiz-Rascado,
César Bonavides-Martínez,
Suzanne M. Paley,
Markus Krummenacker,
Tomer Altman, [......],
Aaron Spaulding,
John Pacheco,
Mario Latendresse,
Carol A. Fulcher,
Malabika Sarker,
Alexander Glennon Shearer,
Amanda Mackie,
Ian T. Paulsen,
Robert P. Gunsalus,
Peter D. Karp
Nucleic Acids Research. 01/2011; 39:583-590.
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Ingrid M Keseler,
Julio Collado-Vides,
Alberto Santos-Zavaleta,
Martin Peralta-Gil,
Socorro Gama-Castro, Luis Muñiz-Rascado,
César Bonavides-Martinez,
Suzanne Paley,
Markus Krummenacker,
Tomer Altman, [......],
Aaron Spaulding,
John Pacheco,
Mario Latendresse,
Carol Fulcher,
Malabika Sarker,
Alexander G Shearer,
Amanda Mackie,
Ian Paulsen,
Robert P Gunsalus,
Peter D Karp
[show abstract]
[hide abstract]
ABSTRACT: EcoCyc (http://EcoCyc.org) is a comprehensive model organism database for Escherichia coli K-12 MG1655. From the scientific literature, EcoCyc captures the functions of individual E. coli gene products; their regulation at the transcriptional, post-transcriptional and protein level; and their organization into operons, complexes and pathways. EcoCyc users can search and browse the information in multiple ways. Recent improvements to the EcoCyc Web interface include combined gene/protein pages and a Regulation Summary Diagram displaying a graphical overview of all known regulatory inputs to gene expression and protein activity. The graphical representation of signal transduction pathways has been updated, and the cellular and regulatory overviews were enhanced with new functionality. A specialized undergraduate teaching resource using EcoCyc is being developed.
Nucleic Acids Research 01/2011; 39(Database issue):D583-90. · 8.03 Impact Factor
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Socorro Gama-Castro,
Heladia Salgado,
Martin Peralta-Gil,
Alberto Santos-Zavaleta, Luis Muñiz-Rascado,
Hilda Solano-Lira,
Verónica Jimenez-Jacinto,
Verena Weiss,
Jair S García-Sotelo,
Alejandra López-Fuentes, [......],
Araceli M Huerta,
Alfredo Mendoza-Vargas,
Leonardo Collado-Torres,
Blanca Taboada,
Leticia Vega-Alvarado,
Maricela Olvera,
Leticia Olvera,
Ricardo Grande,
Enrique Morett,
Julio Collado-Vides
[show abstract]
[hide abstract]
ABSTRACT: RegulonDB (http://regulondb.ccg.unam.mx/) is the primary reference database of the best-known regulatory network of any free-living organism, that of Escherichia coli K-12. The major conceptual change since 3 years ago is an expanded biological context so that transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response. We call these genetic sensory response units, or Gensor Units. We have initiated their high-level curation, with graphic maps and superreactions with links to other databases. Additional connectivity uses expandable submaps. RegulonDB has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry. Several DNA-binding motifs and their sizes have been redefined and relocated. In addition to data from the literature, we have incorporated our own information on transcription start sites (TSSs) and transcriptional units (TUs), obtained by using high-throughput whole-genome sequencing technologies. A new portable drawing tool for genomic features is also now available, as well as new ways to download the data, including web services, files for several relational database manager systems and text files including BioPAX format.
Nucleic Acids Research 11/2010; 39(Database issue):D98-105. · 8.03 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: Genomics, identified as the science of the century, is dramatically changing the historically weak relation between experimental and theoretical biology. ...
Journal of bacteriology 11/2008; 191(1):23-31. · 3.94 Impact Factor
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Socorro Gama-Castro,
Verónica Jiménez-Jacinto,
Martín Peralta-Gil,
Alberto Santos-Zavaleta,
Mónica I Peñaloza-Spinola,
Bruno Contreras-Moreira,
Juan Segura-Salazar, Luis Muñiz-Rascado,
Irma Martínez-Flores,
Heladia Salgado,
César Bonavides-Martínez,
Cei Abreu-Goodger,
Carlos Rodríguez-Penagos,
Juan Miranda-Ríos,
Enrique Morett,
Enrique Merino,
Araceli M Huerta,
Luis Treviño-Quintanilla,
Julio Collado-Vides
[show abstract]
[hide abstract]
ABSTRACT: 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.
Nucleic Acids Research 02/2008; 36(Database issue):D120-4. · 8.03 Impact Factor
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Socorro Gama-Castro,
Verónica Jiménez-Jacinto,
Martín Peralta-Gil,
Alberto Santos-Zavaleta,
Mónica I. Peñaloza-Spínola,
Bruno Contreras-Moreira,
Juan Segura-Salazar, Luis Muñiz-Rascado,
Irma Martínez-Flores,
Heladia Salgado,
César Bonavides-Martínez,
Cei Abreu-Goodger,
Carlos Rodríguez Penagos,
Juan Miranda-Ríos,
Enrique Morett,
Enrique Merino,
Araceli M. Huerta,
Luis Treviño-Quintanilla,
Julio Collado-Vides
Nucleic Acids Research. 01/2008; 36:120-124.
