PPICompare

PPICompare performs differential network analysis of protein-protein interaction (PPI) networks to identify isoform-sensitive rewiring and the transcriptomic drivers of condition-specific interactome changes.

Key Features:

• Detection of Rewiring Events: Identifies statistically significant rewiring events in PPI networks between different cellular states.
• Isoform Sensitivity: Incorporates alternative splicing and isoform-level information to infer condition-specific protein interactions from transcript expression data.
• Transcriptome-Driven Analysis: Infers which transcriptomic alterations explain observed network differences and identifies a minimal set of transcriptomic changes sufficient to account for between-group differences.
• Empirical Findings in Blood Cell Development: Reports significant interactome rewiring during blood cell development and attributes major determinants to differential gene expression while requiring alternative splicing to explain specific stage-to-stage alterations.

Scientific Applications:

• Developmental Biology: Analysis of blood cell development to detect stage-specific PPI rewiring and to dissect contributions of differential expression and alternative splicing.
• Oncology: Investigation of condition-specific PPI network changes to elucidate molecular mechanisms underlying cancer-associated interactome alterations.
• Systems Biology: Integration of transcriptomic data with PPI networks to study global interactome dynamics across biological conditions.

Methodology:

Detects statistically significant PPI rewiring, infers condition-specific interactions from transcript expression with isoform/alternative splicing consideration, and identifies the minimal set of transcriptomic alterations necessary to explain observed between-group network differences.