DeDaL

DeDaL generates data-driven network layouts in Cytoscape 3.0 by integrating multidimensional molecular profiling data with biological network structures to reveal correlation patterns and facilitate interpretation of molecular data in a network context.

Key Features:

• Data-Driven Network Layouts: Constructs biological network layouts by incorporating molecular profile data as node attributes to reflect both network structure and associated multivariate data such as gene expression profiles.
• Dimensionality Reduction: Employs both linear and non-linear dimensionality reduction techniques to transform complex multivariate datasets into layout coordinates driven by underlying data patterns.
• Data Import as Node Attributes: Imports multidimensional molecular profile data and maps them to network nodes for joint structural and data-aware visualization.
• Pre-processing and Post-processing: Includes data pre-processing and layout post-processing steps to prepare profiles and refine generated layouts.
• Morphing and Alignment: Provides continuous morphing between two arbitrary network layouts and alignment operations such as rotation and mirroring for comparative layout analysis.

Scientific Applications:

• Protein–Protein Interaction Network Analysis: Reveals correlation patterns and potential mechanistic insights within large protein-protein interaction networks by combining topology and molecular data.
• Visualization of Gene Expression within Networks: Facilitates exploration of gene expression profiles in the context of network topology to aid interpretation of biological functions and interactions.

Methodology:

DeDaL imports multidimensional molecular profile data as node attributes, applies linear and non-linear dimensionality reduction algorithms to produce layouts that reflect both structural network features and data correlations, and performs layout post-processing including continuous morphing and alignment operations (rotation and mirroring).