RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.

RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of Escherichia coli K-12, including data from both classical molecular biology and high-throughput methodologies. Here, we describe biological advances since our last NAR paper of 2019. We explain the changes to satisfy FAIR requirements.

The EcoCyc Database (2023).

EcoCyc is a bioinformatics database available online at EcoCyc.org that describes the genome and the biochemical machinery of K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of .

The EcoCyc Database in 2021.

The EcoCyc model-organism database collects and summarizes experimental data for K-12. EcoCyc is regularly updated by the manual curation of individual database entries, such as genes, proteins, and metabolic pathways, and by the programmatic addition of results from select high-throughput analyses. Updates to the Pathway Tools software that supports EcoCyc and to the web interface that enables user access have continuously improved its usability and expanded its functionality.

Similarity corpus on microbial transcriptional regulation.

Background: The ability to express the same meaning in different ways is a well-known property of natural language. This amazing property is the source of major difficulties in natural language processing. Given the constant increase in published literature, its curation and information extraction would strongly benefit from efficient automatic processes, for which corpora of sentences evaluated by experts are a valuable resource.

Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes.

Background: Crl, identified for curli production, is a small transcription factor that stimulates the association of the σ factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the transcription rate of genes during the transition from exponential to stationary phase at low temperatures, using indole as an effector molecule. The lack of a comprehensive collection of information on the Crl regulon makes it difficult to identify a dominant function of Crl and to generate any hypotheses concerning its taxonomical distribution in archaeal and bacterial organisms.

Results: In this work, based on a systematic literature review, we identified the first comprehensive dataset of 86 genes under the control of Crl in the bacterium Escherichia coli K-12; those genes correspond to 40% of the σ regulon in this bacterium.

The EcoCyc Database.

EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of .

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0.

Background: Our understanding of the regulation of gene expression has benefited from the availability of high-throughput technologies that interrogate the whole genome for the binding of specific transcription factors and gene expression profiles. In the case of widely used model organisms, such as Escherichia coli K-12, the new knowledge gained from these approaches needs to be integrated with the legacy of accumulated knowledge from genetic and molecular biology experiments conducted in the pre-genomic era in order to attain the deepest level of understanding possible based on the available data.

Results: In this paper, we describe an expansion of RegulonDB, the database containing the rich legacy of decades of classic molecular biology experiments supporting what we know about gene regulation and operon organization in E.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.

EcoCyc (EcoCyc.org) is a freely accessible, comprehensive database that collects and summarizes experimental data for Escherichia coli K-12, the best-studied bacterial model organism. New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc.

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.

RegulonDB (http://regulondb.ccg.unam.

Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12.

Given the current explosion of data within original publications generated in the field of genomics, a recognized bottleneck is the transfer of such knowledge into comprehensive databases. We have for years organized knowledge on transcriptional regulation reported in the original literature of Escherichia coli K-12 into RegulonDB (http://regulondb.ccg.

The EcoCyc Database.

EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the E.

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.

This article summarizes our progress with RegulonDB (http://regulondb.ccg.unam.

EcoCyc: fusing model organism databases with systems biology.

EcoCyc (http://EcoCyc.org) is a model organism database built on the genome sequence of Escherichia coli K-12 MG1655. Expert manual curation of the functions of individual E.

A comparative genome analysis of the RpoS sigmulon shows a high diversity of responses and origins.

The stationary-phase response mediated by the RpoS sigma factor (σ(S), σ³⁸) has been widely studied as a general mechanism of activation of highly diverse genes that maintain cell viability. In bacteria, genes for diverse functions have been associated with this response, showing that bacteria use a large number of functions to contend with adverse conditions in their environment. However, little is known about how the genes have been functionally recruited in diverse organisms.

EcoCyc: a comprehensive database of Escherichia coli biology.

EcoCyc (http://EcoCyc.org) is a comprehensive model organism database for Escherichia coli K-12 MG1655. From the scientific literature, EcoCyc captures the functions of individual E.

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

RegulonDB (http://regulondb.ccg.unam.

EcoCyc: a comprehensive view of Escherichia coli biology.

EcoCyc (http://EcoCyc.org) provides a comprehensive encyclopedia of Escherichia coli biology. EcoCyc integrates information about the genome, genes and gene products; the metabolic network; and the regulatory network of E.

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

RegulonDB (http://regulondb.ccg.unam.

Multidimensional annotation of the Escherichia coli K-12 genome.

The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc assigns biochemical functions to 76%, and 66% of all genes had their functions determined experimentally.

The comprehensive updated regulatory network of Escherichia coli K-12.

Background: Escherichia coli is the model organism for which our knowledge of its regulatory network is the most extensive. Over the last few years, our project has been collecting and curating the literature concerning E. coli transcription initiation and operons, providing in both the RegulonDB and EcoCyc databases the largest electronically encoded network available.

RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.

RegulonDB is the internationally recognized reference database of Escherichia coli K-12 offering curated knowledge of the regulatory network and operon organization. It is currently the largest electronically-encoded database of the regulatory network of any free-living organism. We present here the recently launched RegulonDB version 5.

RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12.

RegulonDB is the primary database of the major international maintained curation of original literature with experimental knowledge about the elements and interactions of the network of transcriptional regulation in Escherichia coli K-12. This includes mechanistic information about operon organization and their decomposition into transcription units (TUs), promoters and their sigma type, binding sites of specific transcriptional regulators (TRs), their organization into 'regulatory phrases', active and inactive conformations of TRs, as well as terminators and ribosome binding sites. The database is complemented with clearly marked computational predictions of TUs, promoters and binding sites of TRs.