Phenome

A phenome is the set of all phenotypes expressed by a cell, tissue, organ, organism, or species. A phenome includes phenotypic traits due to either genetic or environmental influences.

The term "phenome" was independently coined by two groups in the late 1990s (Mahner and Kary, 1997, J Theor Biol, 186, 55-63; Varki et al., 1998, Science, 282, 239-240) [Mahner, M. & Kary, M. (1997) What exactly are genomes, genotypes and phenotypes? And what about phenomes? J Theor Biol, 186, 55-63.] [Varki, A. et al. (1998) Great Ape Phenome Project? Science, 282, 239-240.] and then used in several contexts and publications over the next five years [Paigen, K. & Eppig, J.T. (2000) A mouse phenome project. Mamm Genome, 11, 715-717.] [Nevo, E. (2001) Evolution of genome-phenome diversity under environmental stress. Proc Natl Acad Sci U S A, 98, 6233-6240] [Walhout, A.J. et al. (2002) Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr Biol, 12, 1952-1958] [Freimer, N. & Sabatti, C. (2003) The human phenome project. Nat Genet, 34, 15-21] [Bogue, M. (2003) Mouse Phenome Project: understanding human biology through mouse genetics and genomics. J Appl Physiol, 95, 1335-1337] . Discussions lead 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”(Varki and Altheide, 2005) [Varki, A. & Altheide, T.K. (2005) Comparing the human and chimpanzee genomes: searching for needles in a haystack. Genome Res, 15, 1746-1758] . In practice, the term still lacks a universally accepted definition, and is not yet found in standard dictionaries. Regardless, it is now increasingly used in many scholarly publications.

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. Some examples of human phenotypes are skin color, eye color, height, or specific personality characteristics. Phenotypic differences between individuals can be due to environmental influences, genetic variation such as single nucleotide polymorphisms (SNPs), or a combination of the two. Phenomics is the study of the nature of phenotypes and how they are determined, particularly when studied in relation to the set of all genes (genomics) or all proteins (proteomics).

Footnotes

See also

* -omics
* Bioinformatics
* Phenomics
* Physiome
* Physiomics
* Systems biology
* List of omics topics in biology

External links

* [http://phenome.jax.org/pub-cgi/phenome/mpdcgi?rtn=docs/home Mouse Phenome Project] at the Jackson Laboratory
* [http://phenome.net Phenome.net] : an openfree Phenome portal.