CGHbase

CGHbase manages, analyzes, and visualizes array comparative genomic hybridization (array-CGH) and related microarray data to study genomic copy-number variation.

Key Features:

• Array-CGH Data Management: Stores and organizes array comparative genomic hybridization datasets using a MIAME-compliant MySQL database.
• Multi-Platform Microarray Support: Processes genomic copy-number data generated from multiple microarray platforms.
• Breakpoint Detection Algorithms: Implements computational methods for identifying genomic copy-number breakpoints in array-CGH data.
• Genomic Context Integration: Overlays genomic annotations including genes, segmental duplications, microdeletion regions, and custom tracks within result visualizations.
• Genome Browser Export: Exports analysis results in BED format for visualization in genome browsers such as Ensembl and UCSC Genome Browser.
• SVG-Based Visualization: Uses Scalable Vector Graphics (SVG) to generate detailed visual representations of genomic copy-number data.
• LIMS Data Integration: Links array-CGH datasets with complementary data types such as gene expression profiles.
• Extensible Analysis Architecture: Supports integration of custom analysis modules and visualization components through a plug-in architecture.

Scientific Applications:

• Copy Number Variation Analysis: Detects and analyzes genomic gains and losses in array-CGH experiments.
• Genomic Alteration Studies: Investigates structural genomic variations associated with diseases or developmental processes.
• Integrated Genomic Data Analysis: Combines array-CGH results with gene expression profiles for multi-omics genomic studies.

Methodology:

CGHbase stores array-CGH data in a MIAME-compliant MySQL database, applies breakpoint-detection algorithms to identify copy-number changes, integrates genomic annotations such as genes and segmental duplications, and exports results in formats including BED for genome browser visualization.