GOaGO

GOaGO annotates Gene Ontology terms that are enriched in a given set of gene pairs using a permutation test for overrepresentation of gene pairs associated with a shared term.

Key Features:

• Permutation-based enrichment testing: The enrichment calculation compares gene pair counts in the original set against randomized sets where pair structure is preserved but gene identities and associated terms are permuted.
• Shared term detection: Gene pairs are identified and counted based on their association with a common Gene Ontology term.

Scientific Applications:

• Gene Ontology enrichment analysis of gene pairs: Identification of functionally enriched relationships between genes in paired gene sets.

Methodology:

GOaGO performs a permutation test for overrepresentation of gene pairs associated with a shared Gene Ontology term, counting such pairs in the original set and comparing against randomized sets with preserved pair structure but permuted gene identities and associated terms.