RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
| Autor: | Alfredo José Hernández-Álvarez, Maricela Olvera, Gerardo Salgado-Osorio, Shirley Alquicira-Hernández, Kevin Alquicira-Hernández, Martín Peralta-Gil, Socorro Gama-Castro, Liliana Porrón-Sotelo, Verónica Jiménez-Jacinto, Jair S. García-Sotelo, Lucia Pannier, Verena Weiss, Julio Collado-Vides, Araceli M. Huerta, Alejandra Medina-Rivera, Heladia Salgado, Alejandra López-Fuentes, Leticia Vega-Alvarado, Alberto Santos-Zavaleta, Luis Muñiz-Rascado, César Bonavides-Martínez, Hilda Solano-Lira, Yalbi I. Balderas-Martínez, Aurora Labastida, Irma Martínez-Flores, Enrique Morett, Víctor Del Moral-Chávez |
|---|---|
| Rok vydání: | 2012 |
| Předmět: |
Transcription
Genetic media_common.quotation_subject Genomics Biology Regulon Evolution Molecular Omics data 03 medical and health sciences Upload Bacterial Proteins Databases Genetic Genetics Quality (business) Regulatory Elements Transcriptional Promoter Regions Genetic 030304 developmental biology media_common Internet 0303 health sciences Transcription start Escherichia coli K12 Sequence Analysis RNA 030306 microbiology business.industry Articles Gene Expression Regulation Bacterial Data science Repressor Proteins Quality of evidence The Internet Transcription Initiation Site Transcription (software) business Transcription Factors |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gks1201 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|