This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison, Spring 2012.
What is the Gene Ontology?
Gene ontology covers three areas of gene product properties:
1. cellular component: the parts of a cell or its extracellular environment
2. molecular function: the activities of a gene product at the molecular level (i.e. binding, catalysis)
3. biological process: operations of the gene product in cells, tissues, organs, or organisms
The Gene Ontology (GO) project is an attempt to compile ontology information across species using consistent descriptions. This database is particularly useful in studying SOD1, as it is studied using many model organisms.
1. cellular component: the parts of a cell or its extracellular environment
2. molecular function: the activities of a gene product at the molecular level (i.e. binding, catalysis)
3. biological process: operations of the gene product in cells, tissues, organs, or organisms
The Gene Ontology (GO) project is an attempt to compile ontology information across species using consistent descriptions. This database is particularly useful in studying SOD1, as it is studied using many model organisms.
SOD1 Cellular Component
SOD1 is found principally in the cytoplasm, but has also been shown through various direct assays to be present in the other areas of the cell listed below: [1]
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SOD1 Molecular Function
The flow chart below shows the relationship between the molecular functions of superoxide dismutase. From left to right, the chart shows SOD1 protein binding functions (chaperone binding, protein phosphatase 2B binding, and its own homodimerization), SOD1 zinc and copper ion binding, and its superoxide reductase activity [1]. (Click to enlarge.)
SOD1 Biological Processes
Human SOD1 is associated with 53 widely varying biological processes. The flow chart below shows the relationships between selected biological processes dealing with apoptosis [1].
Analysis
Using AmiGO to search the Gene Ontology database is a simple way to find GO terms that are associated with SOD1 across many organisms. These GO terms are based on data from primary literature, and they place SOD1 into groups with other proteins that have the same cellular component, molecular function and biological processes. Many of the GO terms can be tied to ALS research - SOD1 in the cytoplasm fails to clear superoxide radicals and likely affecting other processes, leading to apoptosis in motor neurons, which is triggered in part through interactions with mitochondrial proteins. With such a wide array of GO terms for cellular component, molecular function and biological process, using flow charts allows for a clear visualization of the connects between them.
1. Ashburner M. et al. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25 (1): 25-9. PMID:10802651