Editing Phenotype (section)

== Genes and phenotypes ==
[[File:Genotype to phenotype.svg|thumb|An organism's phenotype is determined by the sum of its genetic material along with the influence of its environment. This is mediated by a range of biological mechanisms: either the direct activities of gene products or their downstream effects.<ref>{{Cite book |last1=Pakay |first1=Julian |title=Threshold Concepts in Biochemistry |last2=Duivenvoorden |first2=Hendrika |last3=Shafee |first3=Thomas |last4=Clarke |first4=Kaitlin |publisher=La Trobe eBureau |year=2023 |isbn=978-0-6484681-9-6 |doi=10.26826/1017|s2cid=258899183 }}</ref>]]
Phenotypes are determined by an interaction of genes and the environment, but the mechanism for each gene and phenotype is different. For instance, an [[Albinism|albino]] phenotype may be caused by a mutation in the gene encoding [[tyrosinase]] which is a key enzyme in [[melanin]] formation. However, exposure to [[Ultraviolet|UV radiation]] can increase melanin production, hence the environment plays a role in this phenotype as well. For most complex phenotypes the precise genetic mechanism remains unknown. For instance, it is largely unclear how genes determine the shape of bones or the human ear.{{cn|date=March 2023}}

Gene expression plays a crucial role in determining the phenotypes of organisms. The level of gene expression can affect the phenotype of an organism. For example, if a gene that codes for a particular [[enzyme]] is expressed at high levels, the organism may produce more of that enzyme and exhibit a particular trait as a result. On the other hand, if the gene is expressed at low levels, the organism may produce less of the enzyme and exhibit a different trait.<ref>{{cite journal |last1=Oellrich |first1=A. |author2=Sanger Mouse Genetics Project |last3=Smedley |first3=D. |title=Linking tissues to phenotypes using gene expression profiles |journal=Database |date=2014 |volume=2014 |page=bau017 |doi=10.1093/database/bau017|pmid=24634472 |pmc=3982582 }}</ref> Gene expression is regulated at various levels and thus each level can affect certain phenotypes, including [[Transcription (biology)|transcriptional]] and post-transcriptional regulation.{{cn|date=May 2024}}

[[File:Tortie-flame.jpg|thumb|right|alt=tortoiseshell cat|The patchy colors of a tortoiseshell cat are the result of different levels of expression of pigmentation genes in different areas of the skin.]]

Changes in the levels of gene expression can be influenced by a variety of factors, such as environmental conditions, genetic variations, and [[Epigenetics|epigenetic]] modifications. These modifications can be influenced by environmental factors such as diet, stress, and exposure to toxins, and can have a significant impact on an individual's phenotype. Some phenotypes may be the result of changes in gene expression due to these factors, rather than changes in genotype. An experiment involving [[machine learning]] methods utilizing gene expressions measured from RNA sequencing found that they can contain enough signal to separate individuals in the context of phenotype prediction.<ref>{{cite journal |last1=Nussinov |first1=Ruth |last2=Tsai |first2=Chung-Jung |last3=Jang |first3=Hyunbum |title=Protein ensembles link genotype to phenotype |journal=PLOS Computational Biology |date=2019 |volume=15 |issue=6 |page=e1006648 |doi=10.1371/journal.pcbi.1006648|pmid=31220071 |pmc=6586255 |bibcode=2019PLSCB..15E6648N |doi-access=free }}</ref>