Category Cross-Omics>Knowledge Bases/Databases/Tools and Cross- Omics>Pathway Analysis/Gene Regulatory Networks/Tools

Abstract RegulonDB is a reference database offering curated knowledge of the ‘transcriptional regulatory network’ of Escherichia coli K12, currently one of the best-known electronically encoded databases of the ‘genetic regulatory network’ (GRN) of any free-living organism.

A database is a model of a piece of the world. In this sense, RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell.

On the other hand, it is also a model of the organization of the genes in transcription units, operons and simple and complex regulons. In this regard, RegulonDB is a ‘computational model’ of mechanisms of transcriptional regulation.

RegulonDB Contents --

RegulonDB contains detailed information about the different elements that conform to the known regulatory network of the cell, such as transcription factors (TFs), small RNAs (sRNAs) and operon structures with their associated regulatory elements: promoters, TF binding sites and terminators, and attenuators, riboswitches and sRNA targets.

The description of the network contains conceptually enriched precise definitions, such as, simple and complex regulons and regulator classes (global or local and internal or external sensing).

RegulonDB is complemented with, computational analyses and genome- wide predictions of operons, promoters, TF binding sites, ribosome- binding sites and ‘RNA regulatory’ target sites.

Visualizing tools in RegulonDB allow the user to navigate in the genome (Genome browser), to identify co-regulators for a particular TF, to locate the genes’ immediate neighbors in the regulatory network, and to identify sets of genes predicted to be functionally related (Nebulon tool - see below...).

Moreover, it also incorporates tools for the analysis of the transcriptional regulation of global ‘gene expression’ experiments made in E. coli K12 (GETtools - see below...), as well as for exhaustive analyses focused on the detection of ‘regulatory signals’ in upstream regulatory regions (RSA tools - see below...).

RegulonDB is mainly a manual database of regulatory information in E. coli incorporated by a team of curators from the primary literature. PubMed abstracts are selected using a set of pertinent key words related to gene regulation.

When there is direct or suspected new relevant information, the full text of the articles is analyzed and the data are added to RegulonDB and EcoCyc (see G6G Abstract Number 20231).

RegulonDB Classification of evidences (strong and weak) --

The evidences associated to all RegulonDB objects are classified as ‘strong’ or ‘weak’, based on the confidence level of the experiment or prediction that supports objects and their relationships.

A ‘strong’ evidence is assigned to an object when the experimental data provide high certainty of its existence; otherwise, it is a ‘weak’ evidence.

Examples of strong evidences are DNA binding of purified TF for regulatory interactions, mapping of Transcription Start Sites (TSSs) for promoters, and length of mRNA for transcription units.

On the other hand, gene expression analyses and computational predictions are considered ‘weak’ evidences.

It is important to state that several weak evidences for an object do Not become a strong one. These two (2) types of evidences are distinguished graphically with solid or dashed lines for objects supported by strong or weak evidences, respectively.

RegulonDB Tools --

Nebulon Tool -

Nebulon is a system for the ‘inference of functional relationships’ of gene products from the recombination of ‘predicted operons’ across 197 prokaryotic genomes currently available.

The Graphical User Interface (GUI) provides an easy means of navigating through the data at the same time making sense of the data/Functional links.

The manufacturer's hope it will help the scientific community in unraveling ‘novel functional interactions’ thereby improving the annotations of hypothetical/putative genes in many genomes.

There are many available parameters which you can set to get interactions of desired quality.

GETools -

Gene Expression Analysis Tools (GETools) is a web-site that offers a computational environment to analyze the ‘transcriptional regulation’ of global gene expression experiments made in E.coli. The analysis is made mainly by comparisons with the information collected in RegulonDB.

GETools is a set of concatenated and linked programs that extract information to analyze data that come from microarray experiments.

The motivation for these programs is to facilitate a systematic automated comparison between global expression data obtained by current chip and microarray technologies, and whatever knowledge has been gathered from the literature about transcriptional regulation and operon organization from E.coli in RegulonDB.

This web-tool uses information from RegulonDB and from computational predictions done in E.coli K12 to compare them to data from gene expression experiments.

The overall Comparisons include:

1) Operon organization vis-à-vis the transcription profiles;

2) Expression profiles and their consistency with promoter and regulatory signals upstream of the individual genes; as well as

3) A comparison of the set of transcribed genes with an exhaustive set of known and putative transcriptional factors in E.coli.

RSA Tools -

Regulatory Sequence Analysis Tools (RSAT) is a web site that provides a series of ‘modular computer programs’ specifically designed for the detection of regulatory signals in non-coding sequences.

The only input required is a list of genes of interest (e.g. a family of co- regulated genes).

From this information, you can retrieve the upstream sequences over a desired distance, discover putative regulatory signals, search the matching positions for these signals in your original dataset or in whole genomes, and display the results graphically in the form of a ‘feature map’.

Each tool is presented as a form to fill-in. For each form, a manual page provides detailed information about the parameters.

To get familiar with the tools, the manufacturers of these tools recommend you to follow the extensive tutorials provided for these tools on their web- site.

RegulonDB TextPresso Tool -

RegulonDB uses the text-mining tool TextPresso (see G6G Abstract Number 20254) for access to specific gene regulation literature and full papers.

RegulonDB Flowcharts -

The RegulonDB Flowcharts option gives the end-user a good idea of how to use the RegulonDB system and understand its output.

System Requirements

Contact manufacturer.


Manufacturer Web Site RegulonDB

Price Contact manufacturer.

G6G Abstract Number 20568

G6G Manufacturer Number 104175