The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index.
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
Open accessAbstract
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.
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Cites
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Cited by
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Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing
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Metadata
- Authors
- Salgado, H., Peralta-Gil, M., Gama-Castro, S., Santos-Zavaleta, A., Muñiz-Rascado, L., García-Sotelo, J. S., Weiss, V., Solano-Lira, H., Martínez-Flores, I., Medina-Rivera, A., Salgado-Osorio, G., Alquicira-Hernández, S., Alquicira-Hernández, K., López-Fuentes, A., Porrón-Sotelo, L., Huerta, A. M., Bonavides-Martínez, C., Balderas-Martínez, Y. I., Pannier, L., Olvera, M., Labastida, A., Jiménez-Jacinto, V., Vega-Alvarado, L., del Moral-Chávez, V., Hernández-Alvarez, A., Morett, E., & Collado-Vides, J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-11-29
- Volume
- 41
- Issue
- D1
- Pages
- D203-D213
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2121365413
- Cited by
- 425
- References
- 41
- FWCI
- 34.90
- Type
- journal article
- Language
- en
- Open access
- gold
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- Salgado, H., Peralta-Gil, M., Gama-Castro, S., Santos-Zavaleta, A., Muñiz-Rascado, L., García-Sotelo, J. S., Weiss, V., Solano-Lira, H., Martínez-Flores, I., Medina-Rivera, A., Salgado-Osorio, G., Alquicira-Hernández, S., Alquicira-Hernández, K., López-Fuentes, A., Porrón-Sotelo, L., Huerta, A. M., Bonavides-Martínez, C., Balderas-Martínez, Y. I., Pannier, L., . . . Collado-Vides, J. (2013). RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Research. https://doi.org/10.1093/nar/gks1201
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