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Gene Ontologies - GO, Gene Ontologies (GO) - Coggle Diagram
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Gene Ontologies (GO)
Use of controlled vocabularies - provide a way to organize knowledge for subsequent retrieval - useful to build a knowledge organization system
Avoids confusions in cases where multiple things have a common name or one thing has multiple names (alias names)
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Includes terms, definitions and logical relationships (is-a, is-part-of, etc.)
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species.
Provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO.
Useful for enrichment analysis - functional enrichment analysis is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins, and may have an association with disease phenotypes. The method uses statistical approaches to identify significantly enriched or depleted groups of genes. - Can be used for RNA-seq analysis
So, given a set of genes (gene lists) that are up-regulated under certain conditions, an enrichment analysis will find which GO terms are over-represented (or under-represented) using annotations for that gene set.
Annotate genes and gene products, and assimilate and disseminate annotation data.
A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported.
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Computational evidence - based on BLAST hits, etc.
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Tools and databases for GO: AmiGO, HGNC, EggNOG