RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

By S. Gama-Castro, Heladia Salgado, Martín Peralta-Gil, Alberto Santos-Zavaleta, Luis Muñiz-Rascado, Hilda Solano-Lira, V. Jiménez-Jacinto, V. Weiss, J. García-Sotelo, Alejandra López-Fuentes and 18 more. Nucleic Acids Res., 2010

382 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/58bec5aff2ab32dbc68b492c90cc851a67b66fe9

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Citations in the corpus

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection (2012, methodology): “We obtained the gold standard data from RegulonDB [15] (version 7.”
Constraint-based models predict metabolic and associated cellular functions (2014, background): “Interaction networks describe the phenomenological interactions between different biomolecules, including genes 49 , proteins 50 and transcription factors 51 .”
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more (2012, methodology): “Mainly, the TEX exoribonuclease enzyme, which has a preference for 50-monophosphate (50-MP) ends (27), and ligation of synthetic RNA adapters to the whole RNA pool for 50-MP elimination (1) have been used.”
Lag Phase Is a Distinct Growth Phase That Prepares Bacteria for Exponential Growth and Involves Transient Metal Accumulation (2011, positive): “As a positive control, DNA sequences containing the 857 annotated Escherichia coli 70 sites were retrieved from RegulonDB 7.0 (31) and searched using these same parameters.”
Hive plots - rational approach to visualizing networks (2012, methodology): “Using the Escherichia coli RegulonDB [36, 37], a directed gene regulatory network, we will show how HPs can be used to reveal structure.”
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond (2015, background): “We have also enriched the modeling of gene regulation, proposing new concepts, such as regulatory phrases (4) and, more recently, GENSOR units (genetic sensoryresponse units) that link signals, the associated regulatory interactions and the regulated response as metabolic and cellular capabilities (”