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What is an ontology?

An ontology is a hierachical, organized dictionary of terms. It provides a standard set of labels for researchers to apply to genes, and its structure allows for reasoning about terms.

Which ontologies does GREAT provide?

GREAT uses numerous ontologies covering a wide range of topics, which allows you to examine many aspects of your input set. Currently, GREAT includes the Gene Ontology (GO) and other ontologies covering Michael: update list phenotypes and human disease, pathways, protein domains, paralog families, DNA motifs, and gene expression. Specifically, GREAT uses:

Michael: link to a specific page on each ontology

*Phenotypes and Human Disease: MGI Phenotype, MSigDB Cancer Neighborhoods (human only), MSigDB Cancer Modules (human only), MGI Human Disease Browser (human only)
*Gene Ontology
*Pathways: Panther, Pathway Commons, MSigDB Canonical Pathways, BioCyc Pathways
*Protein Domains: InterPro
*Paralog Families: Treefam, GeneFamilyOntology (human only)
*DNA Motifs: MSigDB miRNA Motifs, MSigDB Promoter Motifs, ChIP sets of genes regulated by TFs or miRNAs
*Gene Expression: MGI Expression, Monoallelically Expressed Genes

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