Integrated Overviews

A collection of distributions of the different biological objects encoded in RegulonDB.

Transcriptional Regulatory Network

Different graphic representations (TF-gene, gene-gene, TF-TF, etc.) for the regulatory network of E.coli K12.

Cell Sensing

Internal sensing machinery directs the activity of the regulatory network in Escherichia coli.

RegulonDB and BioNLP research

NLP for facilitating and accelerating curation in RegulonDB and resources for the BioNLP community.

Microbial Conditions Ontology (MCO) Browser

The browser allows the navigation throught the MCO

RegulonDB-HT datasets

High Throughput Dataset Searching Tool

Transcription factor browser

The browser allows the navigation through each transcription factor

Gensor Unit Groups

Access to every curated Gensor Unit

DrawingTracesTool

To display, within a selected region of the genome, other objects contained in RegulonDB or added by the user.

Tracks (JBrowse) for E. coli K12

To display multiple tracks of different datasets using JBrowse.

Tracks (JBrowse) for Shigella flexneri 5a str. M90T

To display multiple tracks of different datasets using JBrowse.

RegulonDB Genome Browser

To navigate through the E. coli genome viewing RegulonDB encoded data.

TF PWMs Browser

The browser allows the navigation through each transcription factors and the distributions that support the quality of PWMs.

Clustering of PWMs

The browser to see the collection of PWMs clustered by their similarity, given the high similarity of motifs of proteins of the same family.

TF Family Browser

The repertoire of TFs where 184 are experimentally described and 120 are predictions. These TFs are classified in different evolutionary families based on PFAM, CDD, and Superfamily annotation.

Coexpression Browser

This section aims to give an overview of the coexpression degree of genes that belong to an operon, a regulon or a strict regulon.

RegulonDB Web Services

RegulonDB Web Services allow developers to access RegulonDB data via SOAP.

Additional Resources

A large organized collection of links to related databases and other resources.

RSA Tools

A collection of tools for regulatory sequence analysis.

Gene Context Tool

To visualize the genomic context of a gene or a group of genes and their orthologous relationships within bacterial genomes.

Gene Expression Analysis Tools

GETools is a computational environment to analyze the transcriptional regulation of gene expression experiments in E.coli.

Promoter Analysis Tools

To analyze promoter regions, generate consensus to polymerase binding sites, and predict putative DNA-promoters in sequences upstream genes of bacterial genomes.