GREAT v1.8 Ontologies

Gene Ontology (GO)

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

Phenotype Data and Human Disease

• Mouse Phenotype - data about mouse genotype - phenotype associations mapped to human genes
• Human Phenotype - data of human phenotypes mapped to human genes
• Disease Ontology - data linking human diseases to associated genes
• 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

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
• Wiki Pathways - zebrafish pathway data

Gene Expression

• 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

Regulatory Motifs

• 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

Gene Families

• 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