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GO terms assigned to a gene product are displayed on the locus page. In this example, GCN4 has been annotated to terms in the molecular function, biological process, and cellular component ontologies. You can find out why this gene product was annotated to these terms by viewing the GO Annotations page for that gene product. The link is located above the list of annotations. Each GO term name is a link to the GO term page that lists other genes at SGD that have been annotated to that term. |
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The GO Annotations page is a detailed description of why a particular GO term was annotated to that gene product. You can access this page from the locus page of the gene. The annotated terms are organized by ontology. The GO term name, the reference providing evidence for that annotation, and the type of evidence is given for each annotation. The GO term name will take you to a page that lists all genes at SGD that have been annotated to that specific GO term. Dates are displayed on the GO annotations page as well. The "assigned on" date indicates when a specific GO term was annotated to the gene product. The "last reviewed" date indicates that date when all the GO terms were reviewed for the gene product. There are multiple types of evidence that can be used to support the GO annotation. A list of evidence codes can be found on the SGD GO help page. A detailed explanation of the evidence codes and their use is found on the GO Consortium website. |
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The GO Term Page lists all genes at SGD that have been annotated to that term. You can access this page from the locus page, from the GO annotations page, or from the results page of an SGD search. Since GO is a controlled vocabulary, the term text string might not be what is commonly used in the literature. In order to clarify the scope of the GO term, the top of the page provides the definition and the ontology of the term. Any synonyms available for the term are also listed in this section of the page. Because the ontologies are represented as a DAG, it is important to see the GO terms in relationship with other terms. The tree view located at the top of the GO term page displays the immediate parents and children of the GO term being viewed. In this example, "transcriptional activator" has a child term. This term is a hyperlink to the GO term page for that term. It is colored brown because there are no genes at SGD directly annotated to that term. The blue arrow is a link to view the parents of the GO term "transcriptional activator". The annotation summary lists any qualifiers (such as NOT, colocalizes_with, contributes_to) that have been used in the annotation. The bottom of this page gives the number of genes annotated to a specific GO term as well as a list of genes with their reference and evidence code(s). Clicking on the gene name will take you to its locus page. In addition, the GO term and its annotation to gene products in other organisms can be viewed in context with the rest of its ontology by going to AmiGO. More information about AmiGO is available in a separate section. |
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In this example, if you chose to see the parents of "transcriptional activator activity" by clicking on the blue arrow, the tree view is adjusted. The GO term of interest is written in red. In addition, its parent GO term and siblings GO terms are displayed. Blue boxes indicated that there are genes at SGD are annotated directly to that term. Brown boxes indicated that no genes at SGD are annotated directly to that term. Each blue and brown box is a hyperlink to the individual GO term page. | |
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| Step 1: All GO terms in the function, process, and component ontologies can be found by searching the SGD database. The Search box (located in all toolbars and on the Search Options Contents page) will find GO terms that match the search criteria. |  |
| Step 2: If the phrase 'transcriptional activator' is entered into the full search, the results page lists the number of matches in the SGD database. In this example, 2 GO terms match the search criteria. The search result is a link to a detailed search results page of the GO terms. If there is only one search result, this page will not be displayed. |  |
| Step 3: The detailed search results page lists each GO term that matches the search criteria. Each match contains the GO term name, the ontology, and all the genes at SGD that are annotated to that term. Clicking on the term name will take you to the GO term page. |  |
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Step 1: An alternative site to search for GO terms is AmiGO. It is maintained by the GO Consortium. It allows the user to see the GO term in context of its ontology and the annotations from databases of many model organisms. This is a cursory overview of AmiGO. Please refer to the AmiGO help page for a more detailed explanation. The AmiGO search box is a wild card search unless the 'exact match' box is selected. |
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Step 2: In its search results, Amigo displays the GO terms that match the search criteria as well as their definitions, if available. The GO term name is a link to a page that lists genes (from multiple model organism databases) that have been annotated to that GO term. For more information on this page, see step 4. An additional feature on the results page at AmiGO is the tree view option. |
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Step 3: The tree view page displays the lineage to every location of the GO term. The number in parentheses indicates how many genes (from multiple databases) that have been annotated to that term. The GO term name links to a page that lists genes (from multiple model organism databases) that have been annotated to that GO term. The ontology can be browsed. A (+) box indicates the children of that term are not displayed. Clicking on the (+) sign expands that branch of the ontology. A (-) box indicates that there are no more children terms. |
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Step 4: The GO term page on AmiGO lists information on the term (including definition and synonyms), the lineage of the term (this tree is not browsable), and all genes annotated to that term. This information is compiled from multiple model organism databases, including SGD. Due to space constraints, this figure only shows a partial list of the genes annotated to 'transcriptional activator'. The list of genes contains links to more information. The gene name is a link to a list of other GO terms annotated to that gene; the database name is a direct link to the gene information at that database; the evidence code is a link to the reference used to annotate the gene. Another feature on the GO term page at AmigGO is the option to view the tree in graphical view. |
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Step 5: AmiGO allows the user to see a graph view of the lineage to the specific term. In this visual display, it is clear how one GO term can have multiple parents. |
| File name | Description |
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| go_term.tab | GO terms and definitions |
| orf_geneontology.tab | All GO annotations for yeast genes. One line per gene. |
| gene_association.sgd | The standard file format for gene_association files of the Gene Ontology (GO) Consortium. May have multiple lines for each gene. A complete description of the file format is available. |
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GO terms can help identify relationships between a large number genes, such as a cluster of genes with similar expression profiles from a microarray experiment. For example, the search results from Expression Connection display the process, function, and component GO terms assigned to that gene. |
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In many cases, genes are assigned to the most detailed GO term available. This makes identifying a common process, function, or component among a group of genes difficult. The GO-Slim Mapping Tool identifies the major branches of the ontologies common to a list of genes or ORFs, based on their GO annotations. The GO terms that represent the major branches of the ontology are higher level terms, also known as GO-Slim terms. The GO-Slim Mapping Tool help page describes how to use the tool and interpret the results. |
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The GO Term Finder is a tool available at SGD that can help identify GO terms that a group of genes has in common. Unlike the GO-Slim Mapping tool which identifies major branches that are common to a group of genes, the GO Term Finder identifies any GO term that is shared among a group of genes, regardless of how granular the term is. The results are viewed graphically so the relationships between the GO terms are displayed. In addition, the results can be downloaded in a tab-delimited file. For more information on the GO Term Finder, please refer to the help page. |
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