Phenome
Encyclopedia
A phenome is the set of all phenotype
s expressed by a cell
, tissue
, organ
, organism
, or species
.
Just as the genome
and proteome
signify all of an organism's genes and proteins, the phenome represents the sum total of its phenotypic traits. Examples of human phenotypic traits are skin color, eye color
, body height, or specific personality
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 polymorphism
s (SNPs), or a combination of these factors.
Phenomics
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
).
Although phenome has been in use for many years, the distinction between the use of phenome and phenotype is problematical. 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[as] a multidimensional search space with several neurobiological levels, spanning the proteome, cellular systems (e.g., signaling pathways), neural systems and cognitive and behavioural phenotypes."
Phenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...
s expressed by a cell
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....
, tissue
Biological tissue
Tissue is a cellular organizational level intermediate between cells and a complete organism. A tissue is an ensemble of cells, not necessarily identical, but from the same origin, that together carry out a specific function. These are called tissues because of their identical functioning...
, organ
Organ (anatomy)
In biology, an organ is a collection of tissues joined in structural unit to serve a common function. Usually there is a main tissue and sporadic tissues . The main tissue is the one that is unique for the specific organ. For example, main tissue in the heart is the myocardium, while sporadic are...
, organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...
, or species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
.
Just as the genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
and proteome
Proteome
The proteome is the entire set of proteins expressed by a genome, cell, tissue or organism. More specifically, it is the set of expressed proteins in a given type of cells or an organism at a given time under defined conditions. The term is a portmanteau of proteins and genome.The term has been...
signify all of an organism's genes and proteins, the phenome represents the sum total of its phenotypic traits. Examples of human phenotypic traits are skin color, eye color
Eye color
Eye color is a polygenic phenotypic character and is 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....
, body height, or specific personality
Personality type
Personality type refers to the psychological classification of different types of individuals. Personality types are sometimes distinguished from personality traits, with the latter embodying a smaller grouping of behavioral tendencies. Types are sometimes said to involve qualitative differences...
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 polymorphism
Single nucleotide polymorphism
A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the genome differs between members of a biological species or paired chromosomes in an individual...
s (SNPs), or a combination of these factors.
Phenomics
Phenomics
Phenomics is an area of biology concerned with the measurement of phenomes — the physical and biochemical traits of organisms — as they change in response to genetic mutation and environmental influences...
is the study of the phenome and how it is determined, particularly when studied in relation to the set of all genes (genomics
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
) or all proteins (proteomics
Proteomics
Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
).
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 problematical. 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
See also
- BioinformaticsBioinformaticsBioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
- PhenomicsPhenomicsPhenomics is an area of biology concerned with the measurement of phenomes — the physical and biochemical traits of organisms — as they change in response to genetic mutation and environmental influences...
- PhysiomePhysiomeThe physiome of an individual's or species'physiological state is the description of itsfunctional behavior. The physiome describes the physiological dynamics ofthe normal intact organism and is built upon information and...
- PhysiomicsPhysiomicsPhysiomics is a systematic study of physiome in biology. Physiomics employs bioinformatics to construct networks of physiological features that are associated with genes, proteins and their networks.-External links:...
- Systems biologySystems biologySystems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses...
- List of omics topics in biology
External links
- Mouse Phenome Project at the Jackson LaboratoryJackson LaboratoryThe Jackson Laboratory was founded in Bar Harbor, Maine in 1929 by former University of Maine and University of Michigan president C. C. Little under the name Roscoe B...