Cascade

Cascade analyzes and predicts temporal responses of gene regulatory networks to environmental stressors and is implemented as an R package.

Key Features:

• Prediction of Gene Expression Changes: Predicts alterations in gene expression levels following biological perturbations within the network.
• Graphical Outputs for Signal Monitoring: Produces graphical outputs that visualize the propagation of signals through the gene regulatory network over time.
• Identification of Influential Genes: Identifies influential genes by analyzing temporal gene interactions to highlight candidates for experimental intervention.

Scientific Applications:

• Modeling network behavior under stress: Models and predicts the behavior of gene regulatory networks in response to environmental stressors.
• Regulatory gene identification: Identifies key regulatory genes that drive network responses to external stimuli.
• Experimental design support: Supports design of experiments aimed at modifying network interactions or testing predicted perturbation effects.

Methodology:

Cascade employs reverse-engineering approaches to construct and analyze gene regulatory networks by inferring network structure and dynamics from observed expression data.