This web page was produced as an assignment for Gen677, an undergraduate course at UW-Madison Spring 2009
Ontologies
There are three types of gene ontologies: biological process, cellular component, and molecular function. Each ontology describes a particular aspect of the gene product. Biological process ontology inherently describe the area(s) that the gene product acts in larger series of events. Cellular component ontology describes what part of the cell the gene product is part of, and molecular function ontology describes specific activities that the gene product is involved in (the Gene Ontology).
Biological Process
SORL1 biological process gene ontology (GO). Red lines indicate that the process higher in the hierarchy is a member of the box directly connected to it and blue lines indicate the process is a part of the larger process it is directly connected to. Human SORL1 locates most specifically as a member of the gene family involved in receptor-mediated endocytosis. Evidence for this relationship is from a traceable author statement (TAS), meaning that this relationship was been published in a citable source. This type of evidence is generally quite good. While there are 166,854 gene products that classify as part of a biological process, only 151 of these gene products that are part of receptor-mediated endocytosis (AmiGO).
The classification of SORL1 makes sense in light of its inferred function in APP protein recycling. A necessary part of this recycling process is endocytosis. Further, since SORL1 is believe to act as a switch in this process, its role in receptor-mediation of this process is aligned with existing knowledge and observations about SORL1.
Cellular Component
According to the GO, integral to plasma membrane means, "Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." The evidence for this relationship is also of the TAS variety. In total, there are 174,600 gene products in the cellular component ontology, 2,483 of which are classified as integral to plasma membrane (AmiGO).
Molecular Function
SORL1 falls into two different molecular function ontologies: low-density lipoprotein (LDL) binding and transmembrane receptor (TMR) activity. The LDL binding ontology has 47 gene products in it and the TMR activity ongology 4,573 of the 253,260 gene products in the molecular function ontology. Evidence for the TMR activity ontology is TAS, but evidence for the LDL binding ontology is IPI, which means it is inferred from physical interaction (AmiGO).
How does Human SORL1 compare with homologs?
A search for SORL1 in the GO generated results only for homo sapiens and rattus norvegicus (norway rat). In the rat species, five associations were found: two in biological process (cell migration and cell proliferation), two in cellular component (cell soma and multivescular body), and one in molecular function (low-density lipoprotein binding) (AmiGO). This is interesting that only one of the GOs is the same as it was in human SORL1, the LDL binding. Perhaps the most interesting difference involves the cellular component. In humans, the cellular component GO association is integral to plasma membrane, whereas in rats the most specific association is multivescular body.
References
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Last Updated 5/13/09
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