AltAnalyze

AltAnalyze analyzes alternative splicing and gene expression using Affymetrix Exon and Gene Array data to identify exon-level changes and interpret their functional consequences.

Key Features:

• Alternative Splicing Detection: Identifies exon-level alternative splicing events using statistical methods including FIRMA (Filtering Inclusion Ratio Model Analysis), MiDAS (Microarray Detection of Alternative Splicing), and DABG (Detection Above Background) filtering.
• Exon and Isoform-Level Analysis: Processes Affymetrix Exon and Gene Array datasets to quantify exon usage and transcript isoform variation.
• Network and Domain Visualization: Integrates with the Cytoscape plugin DomainGraph to visualize isoforms, exons, protein domains, and molecular interaction networks.
• Functional Impact Assessment: Evaluates the effects of alternative exon inclusion on protein domain composition and microRNA binding sites and associates these changes with biological pathways and interaction networks.

Scientific Applications:

• Alternative Splicing Analysis: Detects exon inclusion and exclusion events to study transcript diversity in gene expression datasets.
• Functional Genomics Research: Interprets the structural and regulatory consequences of alternative splicing on proteins and regulatory elements.
• Systems Biology Studies: Links splicing changes to molecular interaction networks and biological pathways.

Methodology:

AltAnalyze processes Affymetrix Exon and Gene Array data to quantify exon expression, applies statistical methods including FIRMA, MiDAS, and DABG filtering to detect alternative splicing events, and integrates Cytoscape DomainGraph visualization to analyze effects on protein domains, microRNA binding sites, and molecular interaction networks.