Information on Transcriptional Regulation and Signal Transduction of _Escherichia coli_ K-12 Integrated in the Database RegulonDB.

Since its inception, RegulonDB ("http://regulondb.ccg.unam.mx/":http://regulondb.ccg.unam.mx/) has been a database that compiles information about the regulation of transcription initiation of _Escherichia coli_ K-12. However, we are aware that transcriptional regulation is not an isolated process; instead, it is the response to the different environmental conditions that trigger a series of concatenated reactions that end in transcriptional regulation, and it implies an adequate response in terms of induced and repressed gene products. We are working now to include all these new data in RegulonDB. As a consequence, transcriptional regulation in RegulonDB will be part of a unit that initiates with the signal, continues with the signal transduction to the core of regulation to modify expression of the affected set of target genes, and ends with an adequate response. We refer to these units as genetic sensory response units, or Gensor Units.

The inclusion of Gensor Units will bring a dramatic change and expansion of RegulonDB, due to the fact that we will be adding several new types of reactions and interactions. We started to collect data about signal transduction of the sigma factors, the two-component systems, of some transcription factors involved in carbon source utilization, and of genes involved in the synthesis of amino acids. We plan a high-level curation with super-pathways summarizing concatenated sets of reactions linked to those other databases that curate such information, while enabling with RegulonDB a compilation of complete Gensor Units.

In addition, the number of DNA binding sites for some transcription factors has grown considerably, and therefore we decided to review systematically those sites whose lengths ranging from 40 to 60 bp with orientation and consensus sequences that are not easy to identify. The current version of RegulonDB is the beginning of a higher-level curation of gene regulation information, and eventually our database will include all regulatory mechanisms and their regulated genes. 
&#xa

Information on Transcriptional Regulation and Signal Transduction of _Escherichia coli_ K-12 Integrated in the Database RegulonDB.

Since its inception, RegulonDB ("http://regulondb.ccg.unam.mx/":http://regulondb.ccg.unam.mx/) has been a database that compiles information about the regulation of transcription initiation of _Escherichia coli_ K-12. However, we are aware that transcriptional regulation is not an isolated process; instead, it is the response to the different environmental conditions that trigger a series of concatenated reactions that end in transcriptional regulation, and it implies an adequate response in terms of induced and repressed gene products. We are working now to include all these new data in RegulonDB. As a consequence, transcriptional regulation in RegulonDB will be part of a unit that initiates with the signal, continues with the signal transduction to the core of regulation to modify expression of the affected set of target genes, and ends with an adequate response. We refer to these units as genetic sensory response units, or geSorgans.

The inclusion of geSorgans will bring a dramatic change and expansion of RegulonDB, due to the fact that we will be adding several new types of reactions and interactions. We started to collect data about signal transduction of the sigma factors, the two-component systems, of some transcription factors involved in carbon source utilization, and of genes involved in the synthesis of amino acids. We plan a high-level curation with super-pathways summarizing concatenated sets of reactions linked to those other databases that curate such information, while enabling with RegulonDB a compilation of complete geSorgans.

In addition, the number of DNA binding sites for some transcription factors has grown considerably, and therefore we decided to review systematically those sites whose lengths ranging from 40 to 60 bp with orientation and consensus sequences that are not easy to identify. The current version of RegulonDB is the beginning of a higher-level curation of gene regulation information, and eventually our database will include all regulatory mechanisms and their regulated genes. 
&#xa

COLOMBOS v2.0 : an ever expanding collection of bacterial expression compendia

The COLOMBOS database (http://www.colombos.net) features comprehensive organism-specific cross-platform gene expression compendia of several bacterial model organisms and is supported by a fully interactive web portal and an extensive web API. COLOMBOS was originally published in PLoS One, and COLOMBOS v2.0 includes both an update of the expression data, by expanding the previously available compendia and by adding compendia for several new species, and an update of the surrounding functionality, with improved search and visualization options and novel tools for programmatic access to the database. The scope of the database has also been extended to incorporate RNA-seq data in our compendia by a dedicated analysis pipeline. We demonstrate the validity and robustness of this approach by comparing the same RNA samples measured in parallel using both microarrays and RNA-seq. As far as we know, COLOMBOS currently hosts the largest homogenized gene expression compendia available for seven bacterial model organisms

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses

open13siCOLOMBOS is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. Compared to the previous version it has more than doubled in size, both in terms of species and data available. The manually curated condition annotation has been overhauled as well, giving more complete information about samples' experimental conditions and their differences. Functionality-wise cross-species analyses now enable users to analyse expression data for all species simultaneously, and identify candidate genes with evolutionary conserved expression behaviour. All the expression-based query tools have undergone a substantial improvement, overcoming the limit of enforced co-expression data retrieval and instead enabling the return of more complex patterns of expression behaviour. COLOMBOS is freely available through a web application at http://colombos.net/. The complete database is also accessible via REST API or downloadable as tab-delimited text files.openMoretto, Marco; Sonego, Paolo; Dierckxsens, Nicolas; Brilli, Matteo; Bianco, Luca; Ledezma-Tejeida, Daniela; Gama-Castro, Socorro; Galardini, Marco; Romualdi, Chiara; Laukens, Kris; Collado-Vides, Julio; Meysman, Pieter; Engelen, KristofMoretto, Marco; Sonego, Paolo; Dierckxsens, Nicolas; Brilli, Matteo; Bianco, Luca; Ledezma Tejeida, Daniela; Gama Castro, Socorro; Galardini, Marco; Romualdi, Chiara; Laukens, Kris; Collado Vides, Julio; Meysman, Pieter; Engelen, Kristo

EcoCyc: a comprehensive database resource for Escherichia coli

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein–ligand interactions

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. A paper published recently by Ma et al. (2004) showed several differences in the versions of the network present in these two databases. Discrepancies have been corrected, annotations from this and other groups (Shen-Orr et al., 2002) have been added, making the RegulonDB and EcoCyc databases the largest comprehensive and constantly curated regulatory network of E. coli K-12. RESULTS: Several groups have been using these curated data as part of their bioinformatics and systems biology projects, in combination with external data obtained from other sources, thus enlarging the dataset initially obtained from either RegulonDB or EcoCyc of the E. coli K12 regulatory network. We kindly obtained from the groups of Uri Alon and Hong-Wu Ma the interactions they have added to enrich their public versions of the E. coli regulatory network. These were used to search for original references and curate them with the same standards we use regularly, adding in several cases the original references (instead of reviews or missing references), as well as adding the corresponding experimental evidence codes. We also corrected all discrepancies in the two databases available as explained below. CONCLUSION: One hundred and fifty new interactions have been added to our databases as a result of this specific curation effort, in addition to those added as a result of our continuous curation work. RegulonDB gene names are now based on those of EcoCyc to avoid confusion due to gene names and synonyms, and the public releases of RegulonDB and EcoCyc are henceforth synchronized to avoid confusion due to different versions. Public flat files are available providing direct access to the regulatory network interactions thus avoiding errors due to differences in database modelling and representation. The regulatory network available in RegulonDB and EcoCyc is the most comprehensive and regularly updated electronically-encoded regulatory network of E. coli K-12

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. coli gene products in EcoCyc has been based on information found in the experimental literature for E. coli K-12-derived strains. Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc

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 5.0 radically different in content, interface design and capabilities. Continuous curation of original scientific literature provides the evidence behind every single object and feature. This knowledge is complemented with comprehensive computational predictions across the complete genome. Literature-based and predicted data are clearly distinguished in the database. Starting with this version, RegulonDB public releases are synchronized with those of EcoCyc since our curation supports both databases. The complex biology of regulation is simplified in a navigation scheme based on three major streams: genes, operons and regulons. Regulatory knowledge is directly available in every navigation step. Displays combine graphic and textual information and are organized allowing different levels of detail and biological context. This knowledge is the backbone of an integrated system for the graphic display of the network, graphic and tabular microarray comparisons with curated and predicted objects, as well as predictions across bacterial genomes, and predicted networks of functionally related gene products. Access RegulonDB at

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. EcoCyc assigns E. coli genes to Gene Ontology and to MultiFun. Seventy-five percent of gene products contain reviews authored by the EcoCyc project that summarize the experimental literature about the gene product. EcoCyc information was derived from 15 000 publications. The database contains extensive descriptions of E. coli cellular networks, describing its metabolic, transport and transcriptional regulatory processes. A comparison to genome annotations for other model organisms shows that the E. coli genome contains the most experimentally determined gene functions in both relative and absolute terms: 2941 (66%) for E. coli, 2319 (37%) for Saccharomyces cerevisiae, 1816 (5%) for Arabidopsis thaliana, 1456 (4%) for Mus musculus and 614 (4%) for Drosophila melanogaster. Database queries to EcoCyc survey the global properties of E. coli cellular networks and illuminate the extent of information gaps for E. coli, such as dead-end metabolites. EcoCyc provides a genome browser with novel properties, and a novel interactive display of transcriptional regulatory networks