netresponse

netresponse discovers organism-wide transcriptional responses within gene interaction networks to reveal context-specific coordinated regulation across tissues.

Key Features:

• Local connected-region discovery: Identifies local, connected regions in biological networks that exhibit coordinated transcriptional responses across subsets of tissues.
• Integration with known interactions: Uses known gene interactions to constrain and guide the network search space.
• Validation on human pathway networks: Validated on human pathway networks, revealing physiologically coherent responses and functional relatedness between tissues.

Scientific Applications:

• Organism-wide modeling: Enables organism-wide modeling of network activation to explore unique and shared mechanisms across tissues.
• Tissue-specific analysis: Detects context-specific transcriptional responses in one or more tissues to study tissue-specific regulatory mechanisms.

Methodology:

Searches for regions within a network that show coordinated transcriptional activity, with the search guided by known gene interactions to limit the analysis scope.