REDfly

REDfly v3.0: Database of Drosophila cis-regulatory modules and transcription factor binding sites

REDfly v3.0 curates empirically validated cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs) in Drosophila melanogaster, integrating regulatory annotations and gene expression data from the literature into a unified database.

Key Features:

• Expanded Regulatory Element Annotations: Includes ~40% more records than previous releases, incorporating new data classes of annotated regulatory elements.
• Integrated REDfly and FlyReg Data: Merges the original REDfly database with the FlyReg TFBS database, providing detailed annotations of validated CRMs and their constituent TFBSs.
• Curated Gene Expression Descriptions: Links each CRM to searchable, literature-derived descriptions of regulated gene expression patterns.
• Computationally Accessible Dataset: Supplies structured regulatory data to support computational analyses of transcriptional regulation in metazoans.

Scientific Applications:

• Comparative Genomics: Analyzes evolutionary conservation and divergence of transcriptional regulatory elements using the Drosophila melanogaster genome.
• Experimental Design Support: Guides functional studies of gene expression control through validated CRM and TFBS annotations.
• Regulatory Sequence Analysis: Enables large-scale computational discovery of CRMs and investigation of regulatory sequence properties and evolution.

Methodology:

REDfly v3.0 compiles and manually curates experimentally validated CRMs and TFBSs from published literature, integrates FlyReg TFBS annotations, classifies regulatory element types, and associates each CRM with documented gene expression patterns to create a structured, searchable repository of Drosophila cis-regulatory data.