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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 phenotypes and human disease, pathways, gene expression, regulatory motifs, and gene families.

To see a description and statistics for an ontology, choose from the list below:

Gene Ontology (GO)

  • GO Biological Process
  • GO Cellular Component
  • GO Molecular Function

Phenotype Data and Human Disease

  • MGI Phenotype
  • MSigDB Cancer Neighborhood
  • MSigDB Cancer Modules

Pathway Data

  • 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

Gene Expression

  • MGI Expression: Detected
  • MGI Expression: Not Detected
  • MSigDB Perturbation

Regulatory Motifs

  • MSigDB miRNA Motifs
  • MSigDB Transcription Factor Motifs
  • miRNA Targets
  • Transcription Factor Targets

Gene Families

  • InterPro
  • TreeFam
  • HGNC Gene Families
  • No labels