Related Experiment Video
Updated: May 11, 2026
08:09
Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
Systematic analysis of experimental phenotype data reveals gene functions.
Robert Hoehndorf1, Nigel W Hardy, David Osumi-Sutherland
1Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom. rh497@cam.ac.uk
Plos One
|April 30, 2013
Summary
We developed a computational method to automatically infer gene functions from observed phenotypes in model organisms. This approach enhances understanding of gene roles and improves predictions of genetic and protein interactions.
Area of Science:
- Genomics
- Computational Biology
- Systems Biology
Background:
- High-throughput phenotyping in model organisms offers insights into gene function.
- Understanding gene function is crucial for deciphering biological processes and organismal roles.
Purpose of the Study:
- To develop and apply a computational, knowledge-based approach for automatic inference of gene functions from phenotypic data.
- To validate the inferred gene functions through manual evaluation and prediction of biological interactions.
Main Methods:
- Utilized a computational, knowledge-based strategy to infer gene functions from phenotypic manifestations.
- Applied the approach to diverse model organisms: yeast, C. elegans, zebrafish, fruitfly, and mouse.
- Analyzed phenotypes using formal definitions from phenotype ontologies.
Main Results:
- Successfully inferred gene functions across multiple model organisms.
- Demonstrated significant improvements in predicting genetic interactions based on functional similarity.
- Showed enhanced prediction of protein-protein interactions using the inferred gene functions.
Conclusions:
- The developed knowledge-based approach effectively infers gene functions from phenotypic data.
- This method is broadly applicable to model organism databases and large-scale phenotyping projects.
- Inferred functions improve the prediction of gene and protein interactions, advancing biological understanding.
Related Concept Videos
01:09Epistasis Analysis
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
02:46Genetic Screens
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
02:27Background and Environment Affect Phenotype
Although the genetic makeup of an organism plays a major role in determining the phenotype, there are also several environmental factors, such as temperature, oxygen availability, presence of mutagens, that can alter an organism’s phenotype.
An example of how genetic background affects phenotype can be seen in horses. The Extension gene in horses is responsible for their coat color. A wild-type gene (EE) produces black pigment in the coat, while a mutant gene (ee) produces red pigment. A...
An example of how genetic background affects phenotype can be seen in horses. The Extension gene in horses is responsible for their coat color. A wild-type gene (EE) produces black pigment in the coat, while a mutant gene (ee) produces red pigment. A...
01:33Pleiotropy
Pleiotropy is the phenomenon in which a single gene impacts multiple, seemingly unrelated phenotypic traits. For example, defects in the SOX10 gene cause Waardenburg Syndrome Type 4, or WS4, which can cause defects in pigmentation, hearing impairments, and an absence of intestinal contractions necessary for elimination. This diversity of phenotypes results from the expression pattern of SOX10 in early embryonic and fetal development. SOX10 is found in neural crest cells that form melanocytes,...
01:39Epistasis
In addition to multiple alleles at the same locus influencing traits, numerous genes or alleles at different locations may interact and influence phenotypes in a phenomenon called epistasis. For example, rabbit fur can be black or brown depending on whether the animal is homozygous dominant or heterozygous at a TYRP1 locus. However, if the rabbit is also homozygous recessive at a locus on the tyrosinase gene (TYR), it will have an unshaded coat that appears white, regardless of its TYRP1...