MIPS mouse functional genome database (MfunGD)

MIPS mouse functional genome database (MfunGD) provides curated and computational functional annotations and protein interaction data for mouse proteins to support analysis of protein networks and functional genomics.

Key Features:

• Manual Annotation: Proteins physically interacting with other proteins are manually curated using evidence from the Mouse Protein-Protein Interaction (MPPI) database and a mammalian protein complexes database.
• Functional Annotation (FunCat): Proteins are systematically classified using the Functional Catalogue (FunCat) annotation scheme for standardized functional assignment.
• Integration with External Resources: Sequence and protein analysis data are cross-referenced with SIMAP Fasta and the Pedant protein analysis system.
• Automated Annotation: Uninspected proteins are annotated automatically using graphical probabilistic models and superparamagnetic clustering.
• Literature Integration: Annotations include references to supporting scientific literature for traceable evidence.
• Technical Implementation: The system is implemented as a J2EE-based component-oriented multi-tier architecture using GenRE software.

Scientific Applications:

• Protein Interaction Studies: Provides curated interaction data and networks to analyze physical protein–protein relationships.
• Functional Genomics: Supports gene function prediction and functional classification of mouse proteins using FunCat and integrated analyses.
• Comparative Analysis: Enables comparative studies by linking annotations and sequence analyses across external resources and protein families.

Methodology:

Annotations combine manual curation supported by MPPI and a mammalian protein complexes database with FunCat functional classification; automated annotation uses graphical probabilistic models and superparamagnetic clustering; sequence and protein analyses leverage SIMAP Fasta and Pedant; the platform runs on a J2EE-based multi-tier architecture using GenRE.