RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

被引：330

作者：

Salgado, Heladia ^{[1
]}

Peralta-Gil, Martin ^{[1
]}

Gama-Castro, Socorro ^{[1
]}

Santos-Zavaleta, Alberto ^{[1
]}

Muniz-Rascado, Luis ^{[1
]}

Garcia-Sotelo, Jair S. ^{[1
]}

Weiss, Verena ^{[1
]}

Solano-Lira, Hilda ^{[1
]}

Martinez-Flores, Irma ^{[1
]}

Medina-Rivera, Alejandra ^{[1
]}

Salgado-Osorio, Gerardo ^{[1
]}

Alquicira-Hernandez, Shirley ^{[1
]}

Alquicira-Hernandez, Kevin ^{[1
]}

Lopez-Fuentes, Alejandra ^{[1
]}

Porron-Sotelo, Liliana ^{[1
]}

Huerta, Araceli M. ^{[1
]}

Bonavides-Martinez, Cesar ^{[1
]}

Balderas-Martinez, Yalbi I. ^{[1
]}

Pannier, Lucia ^{[1
]}

Olvera, Maricela ^{[2
]}

Labastida, Aurora ^{[2
]}

Jimenez-Jacinto, Veronica ^{[3
]}

Vega-Alvarado, Leticia ^{[4
]}

del Moral-Chavez, Victor ^{[1
]}

Hernandez-Alvarez, Alfredo ^{[1
]}

Morett, Enrique ^{[2
]}

Collado-Vides, Julio ^{[1
]}

机构：

[1] Univ Nacl Autonoma Mexico, Ctr Ciencias Genom, Programa Genom Computac, Cuernavaca 62100, Morelos, Mexico

[2] Univ Nacl Autonoma Mexico, Inst Biotecnol, Dept Ingn Celular & Biocatalisis, Cuernavaca 62100, Morelos, Mexico

[3] Univ Nacl Autonoma Mexico, Inst Biotecnol, Unidad Univ Secuenciac Masiva ADN, Cuernavaca 62100, Morelos, Mexico

[4] Univ Nacl Autonoma Mexico, Ctr Ciencias Aplicadas & Desarrollo Tecnol, Grp Vis Artificial & Bioinformat, Mexico City 04510, DF, Mexico

来源：

NUCLEIC ACIDS RESEARCH | 2013年 / 41卷 / D1期

基金：

美国国家卫生研究院;

关键词：

AMP RECEPTOR PROTEIN; FACTOR-BINDING SITES; ESCHERICHIA-COLI; TRANSCRIPTIONAL REGULATION; GENE-REGULATION; RNA-POLYMERASE; PROMOTER; ACTIVATION; EXPRESSION; DKSA;

D O I：

10.1093/nar/gks1201

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

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.

引用

页码：D203 / D213

页数：11

共 46 条

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Regulog analysis:: Detection of conserved regulatory networks across bacteria:: Application to Staphylococcus aureus [J].