BiNGO

BiNGO performs statistical overrepresentation analysis of Gene Ontology (GO) terms for specified gene sets or network-derived subgraphs to identify enriched biological processes, molecular functions, and cellular components.

Key Features:

• GO overrepresentation analysis: Assesses statistical overrepresentation of GO terms within input gene sets or selected network subgraphs.
• GO hierarchy mapping: Maps genes onto the structured Gene Ontology hierarchy, covering biological processes, molecular functions, and cellular components.
• Input modalities: Accepts gene lists as text and analyzes subgraphs derived from biological networks in Cytoscape.
• Cytoscape integration: Integrates with Cytoscape to analyze network subgraphs and produce visual representations of enrichment results.
• Statistical testing: Performs statistical tests to determine which GO categories are significantly overrepresented compared to expectation by chance.
• Implementation: Implemented in Java.

Scientific Applications:

• Functional enrichment of gene sets: Identifies GO terms enriched in gene lists from experimental studies to reveal predominant functional themes.
• Network module characterization: Characterizes functional composition of network-derived modules or subgraphs.
• Genomics and systems biology interpretation: Relates gene sets and network regions to GO categories to aid interpretation of high-level biological functions.

Methodology:

Maps input genes to Gene Ontology terms within the GO hierarchy and performs statistical tests to detect GO categories significantly overrepresented in gene sets or network subgraphs.