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Download TAIR Gene Ontology (GO) Annotations
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TAIR Gene Ontology (GO) Annotations This brief tutorial describes how to access and understand Gene Ontology annotations in TAIR. The Gene Ontology is a set of controlled vocabularies used to describe three qualities of gene products: • Biological process: pathways and larger processes made up of the activities of multiple gene products. • Molecular function: molecular activities of gene products • Cellular component: where gene products are active Using gene ontologies allows us to describe gene function in a way that makes it easier to find and manipulate and analyze computationally. GO also facilitates interoperability because it is the standard used by all sorts of MODS and genome databases. GO annotations are structured associations between gene products that are machine and human readable. They consist of • A gene product (the thing being annotated) • A GO term (function, process or component) • An evidence ‘code’ • A reference for the evidence Evidence codes are short (usually 3 letter codes) that indicate the type of evidence used to support the annotation. • • Experimental Methods o IDA: Inferred from Direct Assay o IGI: Inferred from Genetic Interaction /IGI) Non-experimental Methods (e.g. computational analysis) o RCA: Reviewed Computational Analysis o ISS: Inferred from Structural Similarity What can you do with TAIR GO annotations? • • • • • View all GO annotations for a given locus Search for sets of genes by GO terms Browse the ontologies and find annotations Download GO annotations for a set of genes or the whole genome GO term enrichment using external tools (AMIGO) The locus page shows all of the annotations associated the gene product, grouped according to type. Click on the annotation detail to view a list of all the annotations. Here you can view the essential details of each annotation. • • Click on the reference link to find the paper in which the experiments are described. Or, you want to find similarly annotated genes, you can click on the GO term itself to view the term details and see other genes anntotated to the same term. IN TAIR, you can find genes by GO term in the gene search. Enter in a term. The default search returns all annotations. If you prefer, you can limit the results to only those genes annotated based on experimental evidence. You can also search and browse the ontologies directly by selecting “Ontologies/Keywords” under the Browse menu. You can search for a specific term and then use the tree viewer (click “treeview”) to explore the ontologies. You can choose which types of associated data to display, including annotations, genes or papers. If you have a set of genes that you want to obtain GO Annotations for, you can use the GO Annotation search tool. For example, if you have a list of members of a gene family or co-expressed genes, you can enter the list and download all of the annotations for that gene set. You can also view the results as broader functional categories and display that either as a list or in pie/bar chart formats. You can do this for the whole genome as well as your subset of genes. If you want to do term enrichment to find GO terms that are over represented in a dataset, you can use the Term Enrichment Tool available from the Gene Ontology consortium. TAIR’s annotations are sent to the GO consortium monthly, so you will be accessing the most recent GO annotations from TAIR. Upload your list of locus identifiers and choose A. thaliana as the dataset, and set your set your parameters. For example you may want to restrict your results to only those gene function annotations that are experimentally based, or compare to the whole dataset. We encourage you to learn more about the gene ontologies by visiting the GO website. If you have questions or comments, please email us at [email protected]. For more information about the gene ontologies please visit the Gene Ontology website http://www.Geneontology.org.