PPIXpress

PPIXpress constructs condition-specific protein-protein interaction (PPI) networks by integrating transcript-level expression data and mapping protein interactions to underlying domain interactions to capture effects of alternative splicing on network topology.

Key Features:

• Transcript-Level Data Integration: Integrates transcript-level expression data to tailor PPI network topology to specific cellular conditions.
• Alternative Splicing Consideration: Maps protein interactions to underlying domain interactions to reveal connectivity changes caused by alternative splicing of protein isoforms.
• Condition-Specific Network Construction: Infers presence of specific protein interactions based on the dominant protein isoforms expressed under particular conditions.
• Enhanced Detection of Significant Alterations: Enables comparative analyses, such as matched normal and tumor samples in breast cancer, to identify significant interaction alterations not apparent from gene-level expression alone.

Scientific Applications:

• Systems biology research: Reconstructs context-specific PPI networks to analyze cellular interaction dynamics.
• Oncology / cancerogenesis: Identifies proteins and interaction changes between tumor and normal tissues to study mechanisms of cancer.
• Biomarker and therapeutic target discovery: Highlights altered interactions and isoform-specific connectivity that can point to potential biomarkers or therapeutic targets.

Methodology:

Integration of transcript-level expression data with a comprehensive, condition-unspecific PPI network; mapping individual protein interactions to underlying domain interactions; and inferring condition-specific networks by determining dominant protein isoforms and the presence or absence of interactions.