BiSA

BiSA analyzes transcription factor binding sites and histone modification regions to identify overlapping and proximal genomic features for studies of gene regulation and epigenetic relationships.

Key Features:

• Database Integration: Built on a relational database management system with support for SQL Server on Windows and PostgreSQL on Linux for structured storage and retrieval of genomic data.
• Overlap Analysis: Identifies overlaps among binding patterns using chromosome location, base-pair overlap, or maximum distance between binding peaks.
• Comprehensive Reporting: Reports overlapping regions that share base pairs, nearby and non-overlapping regions, average region sizes, genes proximal to binding sites, and statistical significance of overlaps.
• Visualization: Represents overlapping data as Venn diagrams to visualize intersections among genomic region sets.
• Public Database Access: Connects to an extensive database of publicly available transcription factor binding sites and histone modification data for direct dataset comparison.
• Customizable Analysis: Allows specification of parameters for region overlap and proximity to tailor analyses to research needs.

Scientific Applications:

• Regulatory interaction identification: Detects co-occurring transcription factor binding and histone modification patterns to infer functional relationships between genomic regions.
• Gene regulation studies: Maps binding sites and proximal features to genes to support analyses of regulatory mechanisms affecting gene expression.
• Epigenetic analysis: Compares user datasets with public histone modification and transcription factor binding data to investigate epigenetic influences on gene expression.

Methodology:

Uses a relational database (SQL Server or PostgreSQL) to store genomic intervals; identifies overlaps by chromosome, base-pair overlap, or maximum peak distance; computes average region sizes and statistical significance for overlaps; and generates Venn diagram visualizations.