oppOntology

oppOntology computes enrichment scores across ontology systems to identify overrepresented functional categories in gene lists.

Key Features:

• Enrichment Score Calculation: Calculates enrichment using GeneCount, GeneRatio, EnrichFactor, HypergeometricTest, and FisherExactTest for comprehensive analysis of gene lists.
• Support for Multiple Ontologies: Maps genes to Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Human Phenotype Ontology (HPO), Clusters of Orthologous Groups (COG), Molecular Signatures Database (MsigDB), user-defined functional category databases, and customized GO Slims.
• Batch Processing Capabilities: Performs simultaneous enrichment calculations across multiple samples and supports batch online mapping of KEGG pathway diagrams.

Scientific Applications:

• Functional category identification: Identifies molecular functional categories associated with specific phenotypes in large datasets.
• Translational research and disease mechanism discovery: Supports studies aiming to uncover disease-associated pathways and mechanisms from gene-level data.

Methodology:

Integrates statistical tests (GeneCount, GeneRatio, EnrichFactor, HypergeometricTest, FisherExactTest) with database mappings to GO, KEGG, HPO, COG, MsigDB and user-defined categories, and supports batch processing and KEGG pathway diagram mapping.