FunSimMat

FunSimMat computes functional similarity between genes and proteins using Gene Ontology (GO) annotations to support gene expression analysis, protein function prediction, protein interaction inference, and disease gene prioritization.

Key Features:

• Comprehensive Database: Provides precomputed functional similarity values for proteins listed in UniProtKB and for protein families within Pfam and SMART.
• Enhanced Data Coverage: Integrates additional annotations from the Gene Ontology Annotation project to expand annotation and similarity coverage.
• Semantic Similarity Measures: Supplies multiple semantic similarity measures for GO terms to enable nuanced functional comparisons.
• Disease Gene Prioritization: Implements a Gene Ontology-based method to prioritize candidate disease genes using functional similarity.
• Hierarchical Annotation Classes: Automatically derives a hierarchy of annotation classes to structure and explore functional similarity relationships.

Scientific Applications:

• Gene Expression Analysis: Relates genes by functional similarity to aid interpretation of gene expression patterns and their biological implications.
• Protein Function Prediction: Supports prediction of protein functions based on similarity to annotated proteins.
• Protein Interaction Studies: Infers potential protein interactions and functional relationships from shared GO annotations and similarity scores.
• Disease Research: Assists prioritization of candidate disease genes using GO-based prioritization and functional similarity metrics.

Methodology:

Computes semantic similarity measures for GO terms; precomputes functional similarity values for UniProtKB proteins and Pfam/SMART protein families; incorporates annotations from the Gene Ontology Annotation project; applies a Gene Ontology-based method for disease gene prioritization; automatically derives a hierarchy of annotation classes.