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.
What data does each ontology 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 phenotypes and human disease, pathways, gene expression, regulatory motifs, and gene families.
To see a description and statistics for the current version of an ontology, choose from the list below:
Gene Ontology (GO)
Phenotype Data and Human Disease
- Mouse Phenotype - data about mouse genotype - phenotype associations primarily obtained by curators from the literature
- MSigDB Cancer Neighborhood - gene sets defined by correlated expression profiles with cancer-associated genes
- Zebrafish Phenotype - data about zebrafish genotype - phenotype associations primarily obtained by curators from the literature
- Zebrafish Morpholino Database - data about zebrafish gene - phenotype associations obtained gene knockdowns using morpholinos
- PANTHER Pathway - primarily signaling pathways
- Pathway Commons - a collection of pathways from multiple sources
- BioCyc Pathway - metabolic pathways
- MSigDB Pathway - gene sets from pathway databases
- Wiki Pathways - zebrafish pathway data
- MGI Expression___Detected - genes detected as expressed in data with a focus on gene expression during mouse development
- MSigDB Perturbation - gene sets that change their expression after genetic and chemical perturbations
- Zebrafish Wildtype Expression - genes detected as expressed in wildtype zebrafish during development
- Transcription Factor Targets - genes identified by a transcription factor ChIP-chip experiment
- MSigDB Predicted Promoter Motifs - gene sets that share a transcription factor binding motif
- MSigDB miRNA Motifs - gene sets that share a 3'-UTR microRNA binding motif
- miRNA Targets - genes that are downregulated in a microRNA overexpression experiment
- InterPro - protein domains, families and functional sites
- TreeFam - gene families of paralogs
- HGNC Gene Families - gene sets based on sequence similarity, data from the literature, and manual curation
Previous GREAT version ontology statistics
Can I use other ontologies?
Currently, GREAT only supports the listed ontologies.