Exon Array Analyzer

Exon Array Analyzer identifies alternative splicing events from Affymetrix GeneChip® Exon 1.0 ST Arrays using the Splice Index algorithm.

Key Features:

• Platform support: Processes data generated from Affymetrix GeneChip® Exon 1.0 ST Arrays and accepts CEL files as input.
• Splice detection algorithm: Implements the Splice Index algorithm to detect differentially expressed exons indicative of alternative splicing.
• False-positive reduction: Applies multiple filtering techniques to minimize false positive exon calls.
• Workflow: Processes CEL files through a three-step computational workflow for dataset submission and analysis.
• Annotation output: Produces detailed annotation information linked to detected probe sets and genes.
• Graphical outputs: Generates graphical representations to aid identification of splice events and downstream validation.

Scientific Applications:

• Differential exon expression analysis: Identifies differentially expressed exons across conditions or sample groups.
• Tissue-specific splicing discovery: Enables discovery of tissue-specific alternative splicing, exemplified by analysis of 11 murine tissues and a heart-versus-other comparison that reported 885 differentially expressed probe sets across 649 genes.
• Support for biological validation: Provides annotated and graphical results to guide subsequent experimental validation of splice events.

Methodology:

Processes CEL files through a three-step workflow, applies the Splice Index algorithm to detect differentially expressed exons, implements filtering techniques to reduce false positives, and outputs detailed annotation and graphical representations.