transomics2cytoscape

transomics2cytoscape generates files for 3D transomics visualization by automating the creation of multi-layer KEGG pathway networks with inter-layer edges in Cytoscape.

Key Features:

• KEGG Pathway Layer Integration: Accepts input specifying IDs of multiple KEGG pathway layers with corresponding Z-axis heights for 3D visualization.
• Inter-Layer Edge Definition: Processes edges between pathway layers to represent relationships such as kinase-enzyme interactions across different pathways.
• Cytoscape Automation: Automates network creation using Cytoscape automation (Marth et al., 2019) to generate transomics networks as demonstrated in Yugi et al., 2014.
• 2.5D Visualization: Produces isometric views of stacked X-Y planes for interpretable visualization of trans-omic networks.

Scientific Applications:

• Multi-Omics Data Interpretation: Enables network-based interpretation of multi-omics and trans-omics data in the context of conventional biochemical network layouts.
• Trans-Omic Network Visualization: Supports rapid visualization and frequent updating of trans-omics networks to align with progress in multi-omics/trans-omics data analysis.
• Mechanistic Interpretation: Facilitates mechanistic interpretation of omics data through integrated visualization of multiple molecular layers.

Methodology:

The package takes three inputs: KEGG pathway IDs for each layer, Z-axis heights for each layer, and edge definitions between layers. It generates output files for visualization in Cytoscape using Cytoscape automation.