Ontologizer

Ontologizer performs statistical analysis and visualization of gene or protein sets to identify statistically significant overrepresentation of Gene Ontology (GO) terms.

Key Features:

• Statistical Analysis: Employs the one-sided Fisher's exact test, the parent-child method, and topology-based algorithms to evaluate GO term enrichment.
• Multiple-Testing Correction: Implements several multiple-testing correction procedures to control false positives.
• Visualization Capabilities: Produces graph visualizations of significantly overrepresented GO terms and supports GraphViz for optional rendering.
• Data Exploration: Links GO terms with annotated genes or proteins and enables exploration of relationships between terms and their child terms in the ontology hierarchy.
• Technical Requirements: Requires a Java SE 5.0-compliant runtime environment and optionally GraphViz for graph visualization.

Scientific Applications:

• GO enrichment analysis of large-scale experiments: Identifies functional annotations and biological processes associated with gene or protein sets using Gene Ontology.
• Hypothesis generation and experimental design: Uses GO enrichment results to inform biological hypotheses and guide follow-up experiments.

Methodology:

Performs enrichment testing using one-sided Fisher's exact test, parent-child and topology-based algorithms, applies multiple-testing correction procedures, and visualizes significant GO terms as graphs optionally rendered with GraphViz.