BedSect

BedSect performs intersection, visualization, and functional annotation of genomic regions to analyze transcription factor binding sites (TFBSs), next-generation sequencing (NGS)-derived regions, and other region-based genomic datasets.

Key Features:

• Intersection Analysis: Identifies intersections among multiple genomic region sets, including TFBSs from NGS experiments and public resources such as ENCODE.
• Visualization: Generates publication-ready UpSet plots and correlation plots via an integrated Shiny application to depict subsets and relationships of intersected regions.
• Functional Annotation: Performs gene ontology and pathway enrichment analyses for unique and intersected regions using the GREAT tool.
• Data Integration and Export: Integrates datasets from the Gene Transcription Regulation Database (GTRD), supports incorporation of external region sets, and provides links to view regions as custom tracks in the UCSC Genome Browser.

Scientific Applications:

• Regulatory network analysis: Facilitates study of transcription factor dynamics by intersecting TFBSs with other genomic features to reveal shared regulatory elements.
• Functional interpretation of genomic regions: Enables gene ontology and pathway enrichment of intersected regions to infer biological processes and disease-related functions.

Methodology:

Performs set intersections of genomic regions, generates UpSet and correlation plots via an integrated Shiny application, conducts gene ontology and pathway enrichment using GREAT, integrates GTRD datasets, and outputs links for UCSC Genome Browser custom tracks.