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RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
Open accessAbstract
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.
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Metadata
- Authors
- Gama-Castro, S., Salgado, H., Peralta-Gil, M., Santos-Zavaleta, A., Muniz-Rascado, L., Solano-Lira, H., Jimenez-Jacinto, V., Weiss, V., Garcia-Sotelo, J. S., Lopez-Fuentes, A., Porron-Sotelo, L., Alquicira-Hernandez, S., Medina-Rivera, A., Martinez-Flores, I., Alquicira-Hernandez, K., Martinez-Adame, R., Bonavides-Martinez, C., Miranda-Rios, J., Huerta, A. M., Mendoza-Vargas, A., Collado-Torres, L., Taboada, B., Vega-Alvarado, L., Olvera, M., Olvera, L., Grande, R., Morett, E., & Collado-Vides, J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-11-04
- Volume
- 39
- Issue
- Database
- Pages
- D98-D105
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2054331129
- Cited by
- 353
- References
- 18
- FWCI
- 31.02
- Type
- journal article
- Language
- en
- Open access
- gold
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- Gama-Castro, S., Salgado, H., Peralta-Gil, M., Santos-Zavaleta, A., Muniz-Rascado, L., Solano-Lira, H., Jimenez-Jacinto, V., Weiss, V., Garcia-Sotelo, J. S., Lopez-Fuentes, A., Porron-Sotelo, L., Alquicira-Hernandez, S., Medina-Rivera, A., Martinez-Flores, I., Alquicira-Hernandez, K., Martinez-Adame, R., Bonavides-Martinez, C., Miranda-Rios, J., Huerta, A. M., . . . Collado-Vides, J. (2011). RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Research. https://doi.org/10.1093/nar/gkq1110
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
