Phenome

The phenome is the complete set of phenotypes expressed by an organism, cell, or population. A phenotype is any observable trait, such as morphology, development, physiology, biochemical properties, or behavior. The phenome thus comprises all the observable features that result from interactions between the organism's genotype and its environment over time.

In genetics and systems biology, the phenome contrasts with the genome and with other molecular 'omes' such as the proteome or metabolome. The study of phenomes on a large scale is called phenomics, which uses high-throughput and high-dimensional measurements to characterize phenotypes across many individuals and conditions. The goal is to connect genetic variation to phenotypic variation and to understand how environment, age, and stochastic processes shape trait expression.

Phenomic approaches exploit imaging, spectroscopy, flow cytometry, wearable sensors, and automated assays to capture many traits simultaneously. Data integration with genomic, transcriptomic, proteomic, and metabolomic information supports mapping genotype–phenotype relationships and identifying biomarkers, disease risk factors, or agriculturally important traits.

The concept also emphasizes that the phenome is dynamic and context-dependent; a given genotype may express different phenotypes under different environments or developmental stages. Practical challenges include defining harmonized phenotypes, managing large datasets, and distinguishing causation from correlation in complex traits.