PATH2PPI

PATH2PPI predicts pathway-specific protein-protein interaction (PPI) networks in fully sequenced organisms by transferring interaction information from well-studied reference organisms to infer PPIs within defined biological pathways of less-characterized species.

Key Features:

• Predictive Capability: Infers PPI networks in a target organism by using known protein sets and PPI data from reference organisms.
• Pathway-Specific Analysis: Restricts inference to proteins and interactions within user-specified biological pathways or processes.
• Cross-Species Data Integration: Transfers and integrates protein and interaction information from multiple reference organisms into a single target proteome.
• Implementation: Implemented as an R package.

Scientific Applications:

• Systems Biology: Reconstructs pathway-centered interaction networks to analyze molecular system organization and connectivity.
• Functional Genomics: Supports inference of gene and protein function through predicted pathway-specific interaction partners.
• Drug Discovery and Disease Modeling: Aids identification of pathway-level interaction changes relevant to drug targets and disease mechanisms.
• Evolutionary and Comparative Studies: Facilitates comparative analysis of pathway interactions across species, including non-model organisms.

Methodology:

Maps proteins from well-studied reference organisms onto the target organism's proteome and leverages existing PPI data from those references to predict potential interactions within specified biological pathways.