This web page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison.
Gene Ontology
Ontology is defined as "The hierarchical structuring of knowledge about things by subcategorizing them according to their essential qualities" [1]. Basically, ontology can be understood as placing things into categories based on their characteristics. In Gene Ontology (GO), there are three areas that gene products are categorized within: Biological Process, Cellular Component, and Molecular Function [2]. Biological process refers to a series of events that is accomplished by multiple, ordered molecular interactions [2]. Examples of biological processes that a gene product could be involved in are signal transduction or metabolic process. These examples, and all ontological characteristics, are called GO terms. Molecular function refers to singular activities that occur at the molecular level [2]. GO terms that would fall under the molecular function category are binding activity or transporter activity. Cellular component refers to where in the cell the gene product is located [3]. GO term examples of cellular component are the nucleus or cell membrane.
There are multiple database websites that can be used to search for GO terms: GO Consortium, AMIGO, QUICKGO. GO terms can be used to find proteins that have similar functions or may act in the same pathway. This can be very informative for one trying to determine the cellular and molecular effects of mutating or deleting a gene. Below are the results I obtained by searching TOP3B in QUICKGO.
There are multiple database websites that can be used to search for GO terms: GO Consortium, AMIGO, QUICKGO. GO terms can be used to find proteins that have similar functions or may act in the same pathway. This can be very informative for one trying to determine the cellular and molecular effects of mutating or deleting a gene. Below are the results I obtained by searching TOP3B in QUICKGO.
TOP3B Ontology
Biological Process:
DNA Topological Change Chromosome Segregation |
Molecular Function:
DNA Binding DNA Topoisomerase type I Activity |
Cellular Component:
Condensed Chromosome |
Analysis of TOP3B Ontology
The above GO terms are not surprising, as they all match the function of a topoisomerase protein. I did find it interesting, however, that neither GO consortium or AMIGO returned any GO term results when I searched TOP3B. The only results I could retrieve from those websites were annotations from other protein databases such as UniProt. To me, this signifies that the gene ontology of TOP3B has not been extensively researched and there could be unexpected functions and locations of the TOP3B gene product that have yet to be discovered. This idea is further substantiated by the recent discovery that TOP3B directly binds RNA and proteins [4].
References
[example GO] http://www.nature.com/ng/journal/v43/n2/full/ng.740.html
[1]. Dictionary.com. Ontology. retrieved Apr. 11, 2014. http://dictionary.reference.com/browse/ontology
[2]. the Gene Ontology. An Introduction to the Gene Ontology. retrieved Apr. 11, 2014. http://www.geneontology.org/GO.doc.shtml#ontologies
[3]. Johnson, S. (2011). Gene Ontology (GO) Based Search for Protein Structure Similarity Clustering Metrics. Computer Science Ph.D. Seminar. cs.fit.edu/~dmitra/Compbio/Resources/SteveTalk-GeneOntology.ppt
[4]. Nott, A. The TOP3B way to untangle RNA. Nat. Neurosci. 2013 Sep: 16(9):1163-64.
[BP image] http://www.angelfire.com/sc3/toxchick/celmolbio/celmolbio06.html
[MF image] http://pulpbits.com/5-outline-of-dna-replication/
[CC image] http://www.frontiers-in-genetics.org/page.php?id=hp-2011_en
[1]. Dictionary.com. Ontology. retrieved Apr. 11, 2014. http://dictionary.reference.com/browse/ontology
[2]. the Gene Ontology. An Introduction to the Gene Ontology. retrieved Apr. 11, 2014. http://www.geneontology.org/GO.doc.shtml#ontologies
[3]. Johnson, S. (2011). Gene Ontology (GO) Based Search for Protein Structure Similarity Clustering Metrics. Computer Science Ph.D. Seminar. cs.fit.edu/~dmitra/Compbio/Resources/SteveTalk-GeneOntology.ppt
[4]. Nott, A. The TOP3B way to untangle RNA. Nat. Neurosci. 2013 Sep: 16(9):1163-64.
[BP image] http://www.angelfire.com/sc3/toxchick/celmolbio/celmolbio06.html
[MF image] http://pulpbits.com/5-outline-of-dna-replication/
[CC image] http://www.frontiers-in-genetics.org/page.php?id=hp-2011_en