NetworkAnalys

NetworkAnalys analyzes protein-protein interaction (PPI) networks using gene expression data to identify and characterize differentially expressed genes and network modules for biological interpretation.

Key Features:

• Input data handling: Accepts lists of genes or proteins and single or multiple gene expression datasets.
• Gene annotation and differential expression analysis: Annotates genes and performs differential expression analysis to identify significant genes.
• PPI mapping and network construction: Maps significant genes onto a manually curated PPI database to construct biological networks.
• Network topology and module analysis: Computes network topology metrics and supports module analysis.
• Functional enrichment analysis: Performs enrichment analysis for selected network components.
• Network visualization and export: Produces network visualizations and exports networks in PNG, PDF, and GraphML formats.
• Model organism support: Supports PPI network analysis for human and mouse.

Scientific Applications:

• Comparative network analysis: Analyze PPI-driven differences across cell types and disease states using gene expression data.
• Differential expression-driven network interpretation: Identify and characterize differentially expressed genes within PPI contexts.
• Module and pathway characterization: Detect network modules and interpret their biological functions via functional enrichment.
• Cross-species analysis: Apply PPI network analyses to human and mouse datasets.

Methodology:

Accepts gene/protein lists and expression datasets, performs gene annotation and differential expression analysis, maps significant genes to a manually curated PPI database to construct networks, conducts network topology and module analysis, performs functional enrichment analysis, and exports networks in PNG, PDF, and GraphML.