Drosophila DNase I footprint database

Drosophila DNase I footprint database provides a curated collection of DNase I footprinting-derived transcription factor binding sites in Drosophila melanogaster to support analysis of cis-regulatory sequences and gene regulation.

Key Features:

• Content summary: Contains 1,367 annotated binding sites associated with 87 transcription factors and 101 target genes derived from 201 primary references.
• Experimental basis: Entries originate from DNase I footprinting experimental results rather than purely computational predictions.
• Curation approach: Assembled through systematic literature curation and genome annotation.
• Genome mapping: Binding sites are annotated to locations in the Drosophila melanogaster genome.

Scientific Applications:

• Motif model construction: Use annotated binding sites to build and validate transcription factor motif models.
• Training cis-regulatory module detectors: Provide experimentally derived positive examples for CRM detector training and evaluation.
• Benchmarking alignment tools: Serve as a reference dataset for evaluating sequence alignment and comparative methods.
• Text mining of transcriptional regulation: Support extraction and validation of TF–target relationships in literature-mining efforts for Drosophila.

Methodology:

Compiled by systematic literature curation and genome annotation, extracting DNase I footprinting results from 201 primary references and annotating 1,367 binding sites linked to 87 transcription factors and 101 target genes in the Drosophila melanogaster genome.