TimeNexus

TimeNexus constructs temporal multilayer networks (tMLNs) within Cytoscape by projecting time-series -omics data onto sequential network layers to enable analysis of dynamic regulatory interactions.

Key Features:

• Temporal Integration: Creates and manages tMLNs by encoding time-dependent information in node and edge tables that represent specific time points or intervals.
• Layered Visualization: Represents the multilayer network across all layers, pairs of consecutive layers, or individual layers to inspect temporal changes in network structure.
• Subnetwork Extraction: Enables extraction of active subnetworks through interoperability with PathLinker and AnatApp/ANAT.

Scientific Applications:

• Yeast Cell Cycle Analysis: Identified phase-specific active subnetworks in yeast cell cycle time-series data when used with PathLinker or ANAT.
• Mouse Pain Assay Study: Detected active subnetworks associated with inflammatory responses, including immune response, cell stress response, and apoptosis regulation, from temporal expression data of a mouse hindpaw inflammation assay.

Methodology:

Transforms time-series data into structured node and edge tables, projects these data onto sequential layers corresponding to time points or intervals to form a tMLN, and permits extraction of active subnetworks via PathLinker and AnatApp/ANAT.