Editing Phenotype (section)

==Definition==
{{Redirect|Phenome|the speech unit|Phoneme}}
<!--"Behavioral phenotype" redirects here - do not change this section header without adding "{{Anchor|Definition}}" to the section header (without the quotes); otherwise, your edit will break this redirect.-->

{{Anchor|Definition}}Despite its seemingly straightforward definition, the concept of the phenotype has hidden subtleties. It may seem that anything dependent on the [[genotype]] is a phenotype, including [[molecule]]s such as [[RNA]] and [[protein]]s. Most molecules and structures coded by the genetic material are not visible in the appearance of an organism, yet they are observable (for example by [[Western blot]]ting) and are thus part of the phenotype; human [[Human blood group systems|blood groups]] are an example. It may seem that this goes beyond the original intentions of the concept with its focus on the (living) organism in itself. Either way, the term phenotype includes inherent traits or characteristics that are observable or traits that can be made visible by some technical procedure.{{cn|date=May 2024}}
[[File:ABO Blood Group Phenotypes.jpg|thumb|ABO blood groups determined through a Punnett square and displaying phenotypes and genotypes]]
The term "phenotype" has sometimes been incorrectly used as a shorthand for the phenotypic difference between a mutant and its [[wild type]], which would lead to the false statement that a
"mutation has no phenotype".<ref name="pmid12884976">{{cite journal | vauthors = Crusio WE | title = 'My mouse has no phenotype' | journal = Genes, Brain and Behavior | volume = 1 | issue = 2 | pages = 71 | date = May 2002 | pmid = 12884976 | doi = 10.1034/j.1601-183X.2002.10201.x | s2cid = 35382304 | author-link = Wim Crusio | doi-access = free }}{{cbignore|bot=medic}}</ref>

Behaviors and their consequences are also phenotypes, since behaviors are observable characteristics. <!--"Behavioral phenotype" redirects here - bolded per MOS:BOLD-->'''Behavioral phenotypes''' include cognitive, personality, and behavioral patterns. Some behavioral phenotypes may characterize psychiatric disorders<ref>{{cite journal | vauthors = Cassidy SB, Morris CA | title = Behavioral phenotypes in genetic syndromes: genetic clues to human behavior | journal = Advances in Pediatrics | volume = 49 | pages = 59–86 | date = 2002-01-01 | pmid = 12214780 }}</ref> or syndromes.<ref name="O'Brien&Yule19952">{{Cite book |title=Behavioural Phenotype |publisher=Mac Keith Press |year=1995 |isbn=978-1-898683-06-3 |series=Clinics in Developmental Medicine No.138 | veditors = O'Brien G, Yule W |place=London}}</ref><ref name="O'Brien20022">{{Cite book |url=https://books.google.com/books?id=flz27_U0AhgC&q=%22behavioural+phenotypes+in+clinical+practice%22 |title=Behavioural Phenotypes in Clinical Practice |publisher=Mac Keith Press |year=2002 |isbn=978-1-898683-27-8 | veditors = O'Brien G |place=London |access-date=27 September 2010}}</ref>

A '''phenome''' is the set of all traits expressed by a [[cell (biology)|cell]], [[biological tissue|tissue]], [[organ (anatomy)|organ]], [[organism]], or [[species]]. 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]]."<ref>{{cite journal |author=Davis BD |title=The Isolation of Biochemically Deficient Mutants of Bacteria by Means of Penicillin |journal=[[Proceedings of the National Academy of Sciences of the United States of America]] |volume=35 |issue=1 |pages=1–10 |date=January 1949 |pmid=16588845 |pmc=1062948 |doi= 10.1073/pnas.35.1.1|bibcode=1949PNAS...35....1D |doi-access=free }}</ref> 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.<ref name="JTB1">{{cite journal |vauthors=Loeffler M, Bratke T, Paulus U, Li YQ, Potten CS |title=Clonality and life cycles of intestinal crypts explained by a state dependent stochastic model of epithelial stem cell organization |journal=[[Journal of Theoretical Biology]] |volume=186 |issue=1 |pages=41–54 |date=May 1997 |pmid=9176636 |doi=10.1006/jtbi.1996.0340 |bibcode=1997JThBi.186...41L }}</ref>

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".<ref>{{cite journal |vauthors=Varki A, Altheide TK |title=Comparing the human and chimpanzee genomes: searching for needles in a haystack |journal=[[Genome Research]] |volume=15 |issue=12 |pages=1746–58 |date=December 2005 |pmid=16339373 |doi=10.1101/gr.3737405 |doi-access=free}}</ref> Another team of researchers characterize "the human phenome <nowiki>[as]</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."<ref name="Neuroscience1">{{cite journal |vauthors=Siebner HR, Callicott JH, Sommer T, Mattay VS |title=From the genome to the phenome and back: linking genes with human brain function and structure using genetically informed neuroimaging |journal=[[Neuroscience (journal)|Neuroscience]] |volume=164 |issue=1 |pages=1–6 |date=November 2009 |pmid=19751805 |doi=10.1016/j.neuroscience.2009.09.009 |pmc=3013363}}</ref> Plant biologists have begun to explore the phenome in the study of plant physiology.<ref name="tplants">{{Cite journal|last1=Furbank|first1=Robert T.|last2=Tester|first2=Mark|date=December 2011|title=Phenomics--technologies to relieve the phenotyping bottleneck|journal=Trends in Plant Science|volume=16|issue=12|pages=635–644|doi=10.1016/j.tplants.2011.09.005|issn=1878-4372|pmid=22074787}}</ref> In 2009, a research team demonstrated the feasibility of identifying genotype–phenotype associations using [[electronic health records]] (EHRs) linked to DNA [[biobanks]]. They called this method [[phenome-wide association study]] (PheWAS).<ref>{{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}}</ref>[[File:Pan Y G E.jpg|thumb|384x384px|Exploring relationships among phenotype, genotype and environment at different levels<ref name=":0">{{Cite journal |last1=Guo |first1=Tingting |last2=Li |first2=Xianran |title=Machine learning for predicting phenotype from genotype and environment |journal=Current Opinion in Biotechnology |date=2023 |language=en |volume=79 |pages=102853 |doi=10.1016/j.copbio.2022.102853|pmid=36463837 |s2cid=254211407 |doi-access=free }}</ref>]]
Inspired by the evolution from genotype to genome to [[pan-genome]], a concept of eventually exploring the relationship among pan-phenome, [[pan-genome]], and pan-[[envirome]] was proposed in 2023.<ref name=":0" />

[[File:Biston.betularia.7200.jpg|thumb|''[[Biston betularia]]'' morpha ''typica'', the standard light-colored peppered moth]]
[[File:Biston.betularia.f.carbonaria.7209.jpg|thumb|''B.betularia'' morpha ''carbonaria'', the melanic form, illustrating discontinuous variation]]