RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
| Autor: | Enrique Morett, Irma Martínez-Flores, Liliana Porrón-Sotelo, Alfredo Mendoza-Vargas, Alberto Santos-Zavaleta, Verena Weiss, Blanca Taboada, Verónica Jiménez-Jacinto, Ruth Martínez-Adame, Araceli M. Huerta, Julio Collado-Vides, Hilda Solano-Lira, Leonardo Collado-Torres, Luis Muñiz-Rascado, Juan Miranda-Ríos, Heladia Salgado, Alejandra López-Fuentes, Maricela Olvera, Ricardo Grande, Kevin Alquicira-Hernández, Leticia Olvera, Leticia Vega-Alvarado, Jair S. García-Sotelo, Shirley Alquicira-Hernández, Martín Peralta-Gil, César Bonavides-Martínez, Alejandra Medina-Rivera, Socorro Gama-Castro |
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| Rok vydání: | 2010 |
| Předmět: |
Genetics
Binding Sites Escherichia coli K12 Transcription Genetic Relational database Gene regulatory network Context (language use) Gene Expression Regulation Bacterial Articles Computational biology Biology computer.software_genre Genome Systems Integration Databases Genetic Transcriptional regulation BioPAX : Biological Pathways Exchange Gene Regulatory Networks Transcription Initiation Site Web service Gene computer Signal Transduction Transcription Factors |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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