MoNetFamily

MoNetFamily identifies protein modules, homologous module families, and module-module interaction (MMI) networks across multiple species to analyze protein interactions underlying cellular processes and functional conservation.

Key Features:

• Module Identification: Identifies modules—fundamental units of highly connected proteins—by using BLASTP to search a module template database containing 1785 experimental and 1252 structural templates to detect module candidates for query proteins.
• Homologous Module Inference: Infers homologous modules using protein-protein interaction (PPI) families to assess evolutionary relationships and functional conservation.
• MMI Network Calculation: Statistically calculates module-module interactions (MMIs) and constructs MMI networks based on inferred homologous modules and PPI data.
• Cross-Species Analysis: Identifies neighboring modules and their interactions across species, including Homo sapiens, Mus musculus, and Danio rerio, to compare conserved proteins, PPI profiles, and functional annotations.
• Visualization and Annotation: Visualizes MMI networks (for example, 1818 modules and 9678 MMIs reported for Homo sapiens) and provides query annotations using module families and neighboring modules.

Scientific Applications:

• Module Evolution: Analyzes conservation and divergence of homologous module families across species to study module evolution.
• Cellular Process Analysis: Maps protein modules and MMI networks to elucidate interaction architectures underlying cellular processes and functional organization.

Methodology:

Uses BLASTP searches against a module template database (1785 experimental, 1252 structural templates), infers homologous modules via PPI families, statistically calculates MMIs from inferred modules and PPI data, constructs MMI networks, and identifies neighboring modules across species.