GGB

GGB visualizes high-density genomic data aligned to genome coordinates to enable exploration of regulatory logic, genome organization, transcriptional regulation, and cellular responses.

Key Features:

• Supported data types: Handles data from tiling arrays, ChIP-chip, and high-throughput sequencing methods.
• Genomic alignment visualization: Aligns diverse biological data types by genome coordinates to produce information-rich visualizations.
• Interoperability: Integrates with the Gaggle framework and connects to public repositories containing sequences, interactions, and pathways.
• Data import and storage: Imports large datasets into an in-process database and uses SQL for data management.
• Data manipulation: Uses the R environment for data manipulation of imported datasets.
• Search and navigation: Provides keyword search along with dynamic panning and zooming for navigating genomic regions.
• Annotation bookmarks: Stores bookmarks of genomic locations with descriptive annotations.

Scientific Applications:

• Regulatory logic and transcriptional regulation: Visualizes binding, expression, and other genomic signals to investigate regulatory elements and transcriptional control.
• Integrative analysis of heterogeneous datasets: Relates tiling array, ChIP-chip, and sequencing data within a unified genomic-coordinate framework.
• Integration with public knowledge: Combines sequence, interaction, and pathway data from public repositories for multi-scale analysis.
• Genome organization and cellular responses: Supports comparative visualization to study genome organization and cellular response mechanisms.

Methodology:

Imports tiling array, ChIP-chip, and high-throughput sequencing datasets; stores data in an in-process database using SQL; performs data manipulation in R; aligns multiple data types by genome coordinates; integrates via the Gaggle framework; supports keyword search, dynamic panning and zooming, and bookmark annotations.