phexpo

phexpo performs bidirectional enrichment analysis to identify and characterize statistically significant associations between chemical compounds and human phenotypes for exposome and toxicogenomics research.

Key Features:

• Bidirectional enrichment analysis: Enables analysis from both chemical-to-phenotype and phenotype-to-chemical perspectives.
• Statistical enrichment: Implements enrichment analysis to identify statistically significant chemical–phenotype relationships.
• Curated database integration: Integrates gene annotations from the Comparative Toxicogenomics Database (CTD) and the Human Phenotype Ontology (HPO).
• R package implementation: Provided as an R package for computational analysis.
• Case study examples: Demonstrated links include warfarin and chloroform to specific phenotypes, associations of left ventricular dysfunction, and analyses of polycystic ovary syndrome–related phenotypes with chemicals.
• Bibliographic support: Results are supported by bibliographic references linking findings to the scientific literature.

Scientific Applications:

• Exposome research: Characterizes how environmental chemicals associate with human phenotypic outcomes.
• Toxicogenomics: Identifies chemical–phenotype associations relevant to toxicological response and mechanism studies.
• Pharmacology: Links drug compounds such as warfarin to phenotype manifestations for drug-effect analysis.
• Personalized medicine: Supports investigation of phenotype-specific chemical exposures that may influence individual health outcomes.
• Gene–environment interplay studies: Facilitates analysis of interactions between genetic annotations and environmental chemical exposures.

Methodology:

Performs bidirectional enrichment analysis integrating CTD and HPO gene annotations to systematically identify statistically significant chemical–phenotype associations.