RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
Heladia Salgado,Martín 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,Gerardo Salgado-Osorio,Shirley Alquicira-Hernández,Kevin Alquicira-Hernández,Alejandra López-Fuentes,Liliana Porrón-Sotelo,Araceli M. Huerta,César Bonavides-Martínez,Yalbi I. Balderas-Martínez,Lucia Pannier,Maricela Olvera,Aurora Labastida,Verónica Jiménez-Jacinto,Leticia Vega-Alvarado,Víctor Del Moral-Chávez,Alfredo José Hernández-Álvarez,Enrique Morett,Julio Collado-Vides +26 more
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TLDR
RegulonDB version 8.0 is a much better home for integrating knowledge on gene regulation from the sources of information currently available, particularly for knowledge generated through high-throughput (HT) technology.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.read more
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Conflict of interest statement. None declared.
TL;DR: It is found that women over 50 are more likely to have a family history of diabetes, especially if they are obese, than women under the age of 50.
Journal ArticleDOI
Antibiotics induce redox-related physiological alterations as part of their lethality
Daniel J. Dwyer,Peter Belenky,Jason H. Yang,I. Cody MacDonald,Jeffrey D. Martell,Noriko Takahashi,Clement T Y Chan,Michael A. Lobritz,Dana Braff,Eric G. Schwarz,Jonathan D. Ye,Mekhala Pati,Maarten Vercruysse,Paul S. Ralifo,Kyle R. Allison,Ahmad S. Khalil,Alice Y. Ting,Graham C. Walker,James J. Collins +18 more
TL;DR: This work provides direct evidence that, downstream of their target-specific interactions, bactericidal antibiotics induce complex redox alterations that contribute to cellular damage and death, thus supporting an evolving, expanded model of antibiotic lethality.
Journal ArticleDOI
The quantitative and condition-dependent Escherichia coli proteome.
Alexander Schmidt,Karl Kochanowski,Silke R Vedelaar,Erik Ahrné,Benjamin Volkmer,Luciano Callipo,Kèvin Knoops,Manuel Bauer,Ruedi Aebersold,Ruedi Aebersold,Matthias Heinemann +10 more
TL;DR: This work uses efficient protein extraction and sample fractionation, as well as state-of-the-art quantitative mass spectrometry techniques to generate a comprehensive, condition-dependent protein-abundance map for Escherichia coli, uncovering system-wide proteome allocation, expression regulation and post-translational adaptations.
Journal ArticleDOI
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
Socorro Gama-Castro,Heladia Salgado,Alberto Santos-Zavaleta,Daniela Ledezma-Tejeida,Luis Muñiz-Rascado,Jair S. García-Sotelo,Kevin Alquicira-Hernández,Irma Martínez-Flores,Lucia Pannier,Jaime A. Castro-Mondragon,Alejandra Medina-Rivera,Hilda Solano-Lira,César Bonavides-Martínez,Ernesto Pérez-Rueda,Shirley Alquicira-Hernández,Liliana Porrón-Sotelo,Alejandra López-Fuentes,Anastasia Hernández-Koutoucheva,Víctor Del Moral-Chávez,Fabio Rinaldi,Julio Collado-Vides +20 more
TL;DR: The semiautomatic strategy to accelerate curation, including datasets from high-throughput experiments, a novel coexpression distance to search for ‘neighborhood’ genes to known operons and regulons, and computational developments are described.
Journal ArticleDOI
iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition.
TL;DR: It was discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the σ54 promoters.
References
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Conflict of interest statement. None declared.
TL;DR: It is found that women over 50 are more likely to have a family history of diabetes, especially if they are obese, than women under the age of 50.
Journal ArticleDOI
The Generic Genome Browser: A Building Block for a Model Organism System Database
Lincoln Stein,Christopher J. Mungall,ShengQiang Shu,Michael Caudy,Marco Mangone,Allen Day,Elizabeth Nickerson,Jason E. Stajich,Todd W. Harris,Adrian Arva,Suzanna E. Lewis +10 more
TL;DR: The Generic Genome Browser (GBrowse) is described, a Web-based application for displaying genomic annotations and other features and easy integration with other components of a model organism system Web site.