A phenome, similar to
phenotype
In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological pr ...
, is the set of all traits expressed by a
cell
Cell most often refers to:
* Cell (biology), the functional basic unit of life
Cell may also refer to:
Locations
* Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery ...
,
tissue,
organ,
organism
In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and ...
, or
species
In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...
.
Just as the
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...
and
proteome
The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. ...
signify all of an organism's genes and proteins, the phenome represents the sum of its phenotypic traits. Examples of human phenotypic traits are
skin color
Human skin color ranges from the darkest brown to the lightest hues. Differences in skin color among individuals is caused by variation in pigmentation, which is the result of genetics (inherited from one's biological parents and or individu ...
,
eye color
Eye color is a polygenic phenotypic character determined by two distinct factors: the pigmentation of the eye's iris and the frequency-dependence of the scattering of light by the turbid medium in the stroma of the iris.
In humans, the ...
,
body height, or specific
personality
Personality is the characteristic sets of behaviors, cognitions, and emotional patterns that are formed from biological and environmental factors, and which change over time. While there is no generally agreed-upon definition of personality, m ...
characteristics. Although any phenotype of any organism has a basis in its genotype, phenotypic expression may be influenced by environmental influences, mutation, and genetic variation such as
single nucleotide polymorphisms (SNPs), or a combination of these factors.
Phenomics Phenomics is the systematic study of traits that make up a phenotype, and was coined by UC Berkeley and LBNL scientist Steven A. Garan. As such, it is a transdisciplinary area of research that involves biology, data sciences, engineering and othe ...
is the study of the phenome and how it is determined, particularly when studied in relation to the set of all genes (
genomics) or all proteins (
proteomics).
Origin and usage
The term was first used by Davis in 1949, "We here propose the name ''phenome'' for the sum total of extragenic, non-autoreproductive portions of the cell, whether cytoplasmic or nuclear. The phenome would be the material basis of the phenotype, just as the genome is the material basis of the genotype."
Although phenome has been in use for many years, the distinction between the use of phenome and phenotype is problematic. A proposed definition for both terms as the "physical totality of all traits of an organism or of one of its subsystems" was put forth by Mahner and Kary in 1997, who argue that although scientists tend to intuitively use these and related terms in a manner that does not impede research, the terms are not well defined and usage of the terms is not consistent.
Some usages of the term suggest that the phenome of a given organism is best understood as a kind of matrix of data representing physical manifestation of phenotype. For example, discussions led by A.Varki among those who had used the term up to 2003 suggested the following definition: “The body of information describing an organism's phenotypes, under the influences of genetic and environmental factors”. Another team of researchers characterize "the human phenome
s/nowiki> a multidimensional search space with several neurobiological levels, spanning the proteome, cellular systems (e.g., signaling pathways), neural systems and cognitive and behavioural phenotypes."electronic health records
An electronic health record (EHR) is the systematized collection of patient and population electronically stored health information in a digital format. These records can be shared across different health care settings. Records are shared throu ...
(EHRs) linked to DNA biobanks
A biobank is a type of biorepository that stores biological samples (usually human) for use in research. Biobanks have become an important resource in medical research, supporting many types of contemporary research like genomics and personalize ...
. They called this method phenome-wide association study
In genetics and genetic epidemiology, a phenome-wide association study, abbreviated PheWAS, is a study design in which the association between single-nucleotide polymorphisms or other types of DNA variants is tested across a large number of dif ...
(PheWAS).[{{Cite journal, last1=Denny, first1=Joshua C., last2=Ritchie, first2=Marylyn D., last3=Basford, first3=Melissa A., last4=Pulley, first4=Jill M., last5=Bastarache, first5=Lisa, last6=Brown-Gentry, first6=Kristin, last7=Wang, first7=Deede, last8=Masys, first8=Dan R., last9=Roden, first9=Dan M., last10=Crawford, first10=Dana C., date=2010-05-01, title=PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations, journal=Bioinformatics, volume=26, issue=9, pages=1205–1210, doi=10.1093/bioinformatics/btq126, issn=1367-4811, pmc=2859132, pmid=20335276]
See also
* Bioinformatics
* Phenomics Phenomics is the systematic study of traits that make up a phenotype, and was coined by UC Berkeley and LBNL scientist Steven A. Garan. As such, it is a transdisciplinary area of research that involves biology, data sciences, engineering and othe ...
* Physiome The physiome of an individual's or species' physiological state is the description of its functional behavior. The physiome describes the physiological dynamics of the normal intact organism and is built upon information and
structure (genome, prote ...
* Physiomics
* Systems biology
* List of omics topics in biology
Inspired by the terms genome and genomics, other words to describe complete biological datasets, mostly sets of biomolecules originating from one organism, have been coined with the suffix '' -ome'' and ''-omics''. Some of these terms are related ...
References
External links
Mouse Phenome Project
at the Jackson Laboratory
Systems biology
Bioinformatics
Omics
Phenomics