Diffusion

Diffusion propagates signals across biological interaction networks to prioritize genes, predict protein functions, and stratify patients using network propagation within Cytoscape.

Key Features:

• Integration with Cytoscape: Implements network propagation as a Cytoscape application operating on Cytoscape network objects.
• Network propagation algorithm: Simulates diffusion of information across networks to spread initial signals and identify related nodes.
• Use of initial signals: Accepts initial signals such as known disease-related genes and propagates them to rank genes or proteins by network proximity.
• Demonstrated application: Has been used to identify mutations associated with resistance to the drug Vemurafenib.

Scientific Applications:

• Protein Function Prediction: Infers protein functions by propagating annotations through interaction networks to identify functionally related proteins.
• Disease Gene Prioritization: Ranks candidate disease genes by spreading disease-associated signals through gene and protein interaction networks.
• Patient Stratification: Supports stratification of patients based on network-based analysis of genetic profiles.

Methodology:

Employs a network propagation algorithm that simulates diffusion of information across a biological network by spreading initial signals (e.g., known disease-related genes) to identify other relevant nodes (genes or proteins).