RegulonDB

RegulonDB curates and integrates regulatory data for Escherichia coli K-12 to characterize its transcriptional regulatory network.

Key Features:

• Gensor Units: Represents transcriptional regulation as cohesive genetic sensory response units that span signal initiation, signal transduction, and regulatory mechanisms altering gene expression.
• Transcription factor curation: Provides meticulously curated summaries for each transcription factor (TF) and their corresponding binding sites, including annotations of internal symmetry.
• DNA-binding motif refinement: Redefines DNA-binding motif sizes and genomic locations based on literature data and insights derived from high-throughput whole-genome sequencing technologies.
• TSS and TU annotation: Contains detailed information on transcription start sites (TSSs) and transcriptional units (TUs) to enhance regulatory annotations.
• Network maps and superreactions: Supplies graphic maps, superreactions, and expandable submaps that are interconnected with other databases to represent complex regulatory interactions.
• Data export formats: Offers data access via web services, files compatible with several relational database management systems, and text files in BioPAX format.

Scientific Applications:

• Regulatory network characterization: Enables mapping and analysis of the Escherichia coli K-12 transcriptional regulatory network.
• TF–binding site analysis: Supports analysis and interpretation of transcription factor binding sites and symmetry annotations.
• Motif validation with sequencing: Facilitates refinement and validation of DNA-binding motifs using literature and whole-genome sequencing data.
• Transcript annotation: Supports annotation and study of transcription start sites and transcriptional units.
• Cross-database integration: Allows integration of regulatory information with external databases and pathway-level constructs via superreactions and maps.

Methodology:

Motif sizes and locations refined by literature curation and whole-genome sequencing data; construction of graphic maps, superreactions, and expandable submaps interconnected with external databases; data provided via web services, relational database-compatible files, and BioPAX text files.