VisANT

VisANT enables integration, visualization, and analysis of biomolecular interaction networks and pathways to support pathway analysis, systems biology, and network-based disease and drug research.

Key Features:

• Integration with databases: Direct integration with GenBank, KEGG, SwissProt, Gene Ontology (GO), Stanford Microarray Database (SMD), and Gene Expression Omnibus (GEO) for access to published biomolecular interaction and expression datasets.
• Multi-tiered architecture: Implements a multi-tiered architecture that separates data retrieval from visualization.
• Visualization and annotation: Multi-scale visualization, editing, and annotation using KEGG-compatible visual notation with expression data represented via color intensity or embedded expression profiles within nodes.
• Import formats and extensibility: Supports import of network data in PSI-MI and BioPAX formats and provides an open API for Java-based plug-ins.
• Gene Ontology integration and analysis: Tree-based GO browser with flexible annotation schemas and algorithms to detect over-represented GO terms and expression-enriched GO modules within sub-networks while considering network topology.
• Disease and drug network analysis: Support for disease and drug hierarchies, association networks for diseases-genes, therapies-drugs, and drug-targets, enrichment analysis to predict associated diseases or therapies for genes/drugs, and network transformation to construct models linking drugs, genes, diseases, and therapies.

Scientific Applications:

• Exploratory pathway analysis: Visualization and multi-scale interrogation of metabolic and signaling pathways using KEGG-compatible notation and integrated datasets.
• Systems biology and gene regulation: Analysis of gene regulation and molecular interaction networks with embedded expression profiling and topology-aware GO module detection.
• Network-based disease and drug research: Construction and enrichment-based analysis of disease–gene, therapy–drug, and drug–target networks to support drug repositioning and combination therapy design.

Methodology:

Integrates data from GenBank, KEGG, SwissProt, GO, SMD, and GEO; ingests PSI-MI and BioPAX network formats; uses a multi-tiered data-retrieval/visualization architecture; performs multi-scale visualization with KEGG-compatible notation and node-level expression mapping (color intensity or embedded profiles); provides a GO tree browser and topology-aware algorithms for over-represented GO term and expression-enriched GO module detection; applies enrichment analysis for disease/therapy association prediction and supports network transformations to build models linking drugs, genes, diseases, and therapies; exposes a Java-based plug-in API.