ProphTools

ProphTools performs prioritization on heterogeneous biological networks to identify and rank candidate genes, long noncoding RNAs (lncRNAs), and drug targets using network propagation algorithms.

Key Features:

• Heterogeneous network representation: Defines prioritization problems with an arbitrary number of entity types and their interconnections within a single network model.
• Flow propagation algorithm: Implements a flow propagation algorithm inspired by Random Walk with Restarts to propagate information across network nodes.
• Weighted propagation method: Incorporates varying importance of connections and entities via a weighted propagation scheme to refine prioritization scores.
• Hybrid propagation approach: Combines flow propagation and weighted propagation methods into a hybrid strategy for heterogeneous network analysis.
• Cross-validation functionality: Provides cross-validation tests to evaluate and select optimal network configurations for specific datasets.

Scientific Applications:

• Gene-disease prioritization: Ranks genes associated with particular diseases by propagating association signals through the heterogeneous network.
• Drug repositioning: Identifies candidate drugs for repositioning by analyzing network relationships among drugs, targets, and disease entities.
• lncRNA-disease prioritization: Applies prioritization to long noncoding RNAs (lncRNAs) and in a proof-of-concept matched the performance of specialized prioritization tools while remaining general across entity types.

Methodology:

Implements a hybrid approach combining flow propagation (inspired by Random Walk with Restarts) and weighted propagation methods, and supports cross-validation to evaluate network configurations.