A-DaGO-Fun

A-DaGO-Fun performs Gene Ontology (GO) semantic similarity-based functional analyses to compute and quantify functional relatedness between genes and gene sets for biological knowledge discovery.

Key Features:

• Integration of Semantic Similarity Measures: Incorporates all known information content-based semantic similarity measures derived from the Gene Ontology framework.
• Computation and Manipulation of GO-based Measures: Computes, manipulates, and explores GO-based semantic similarity measures for genes and gene sets.
• Customization and Adaptability: Allows selection and adaptation of semantic similarity approaches to suit specific biological applications.
• Comprehensive Data Handling: Handles datasets from high-throughput genome-wide studies for large-scale functional analyses.

Scientific Applications:

• Functional Annotation: Enhances gene annotation by identifying functional similarities based on GO terms.
• Gene Set Enrichment Analysis: Supports identification of enriched biological processes or pathways within gene sets derived from experimental data.
• Disease Research: Investigates genetic contributions to disease by comparing functional similarity among disease-associated genes.
• Comparative Genomics: Compares functional similarities across species or strains to assess functional conservation and divergence.

Methodology:

Integrates Gene Ontology annotations into analysis workflows and employs information content-based semantic similarity measures derived from the Gene Ontology to quantitatively assess functional relatedness between genes or gene sets.