GREAT v1.8 Ontologies

Gene Ontology (GO)

• GO Molecular Function v1.8
• GO Biological Process v1.8
• GO Cellular Component v1.8

Phenotype Data and Human Disease

• Mouse Phenotype v1.8 - data about mouse genotype - phenotype associations mapped to human genes
• Human Phenotype v1.8 - data of human phenotypes mapped to human genes
• Disease Ontology v1.8 - data linking human diseases to associated genes
• MSigDB Cancer Neighborhood v1.8 - gene sets defined by correlated expression profiles with cancer-associated genes
• Zebrafish Phenotype v1.8 - data about zebrafish genotype - phenotype associations primarily obtained by curators from the literature

Pathway Data

• PANTHER Pathway v1.8 - primarily signaling pathways
• Pathway Commons v1.8 - a collection of pathways from multiple sources
• BioCyc Pathway v1.8 - metabolic pathways
• MSigDB Pathway v1.8 - gene sets from pathway databases
• Wiki Pathways v1.8 - zebrafish pathway data

Gene Expression

• MGI Expression Detected v1.8 - genes detected as expressed in data with a focus on gene expression during mouse development
• MSigDB Perturbation v1.8 - gene sets that change their expression after genetic and chemical perturbations
• Zebrafish Wildtype Expression v1.8 - genes detected as expressed in wildtype zebrafish during development

Regulatory Motifs

• Transcription Factor Targets v1.8 - genes identified by a transcription factor ChIP-chip experiment
• MSigDB Predicted Promoter Motifs v1.8 - gene sets that share a transcription factor binding motif
• MSigDB miRNA Motifs v1.8 - gene sets that share a 3'-UTR microRNA binding motif
• miRNA Targets v1.8 - genes that are downregulated in a microRNA overexpression experiment

Gene Families

• InterPro v1.8 - protein domains, families and functional sites
• TreeFam v1.8 - gene families of paralogs
• HGNC Gene Families v1.8 - gene sets based on sequence similarity, data from the literature, and manual curation