PathwayMatrix

PathwayMatrix visualizes protein and molecular activation pathways using an adjacency matrix to facilitate analysis of biochemical reaction networks and protein–molecule relationships.

Key Features:

• Adjacency matrix representation: Uses an adjacency matrix to represent relationships between proteins and molecules within activation pathways.
• Filtering capabilities: Provides filters to focus analysis on specific proteins or biochemical reactions within large pathway networks.
• Lensing and clustering: Supports lensing to magnify pathway regions and clustering to group related proteins or interactions for pattern identification.
• Brushing and linking: Implements brushing and linking to coordinate selections across multiple views and reveal linked relationships within pathways.

Scientific Applications:

• Systems biology analysis: Enables systems biologists to analyze signaling pathway topology and inter-protein relationships in complex networks.
• Cancer signaling research: Assists cancer researchers in examining signaling pathways to identify dysregulated interactions relevant to oncogenesis.
• Hypothesis generation and target exploration: Facilitates identification of patterns and relationships to support hypothesis generation and exploration of potential therapeutic targets.

Methodology:

Evaluated through in-depth interviews with domain experts.