GREAT v1.2 Ontologies

Gene Ontology (GO)

• GO Molecular Function v1.2
• GO Biological Process v1.2
• GO Cellular Component v1.2

Phenotype Data and Human Disease

• Mouse Phenotype v1.2 - data about mouse genotype - phenotype associations primarily obtained by curators from the literature
• MSigDB Cancer Neighborhood v1.2 - gene sets defined by correlated expression profiles with cancer-associated genes
• MSigDB Cancer Modules v1.2 - gene sets with an altered expression in a variety of cancer conditions

Pathway Data

• PANTHER Pathway v1.2 - primarily signaling pathways
• Pathway Commons v1.2 - a collection of pathways from multiple sources
• BioCyc Pathway v1.2 - metabolic pathways
• MSigDB Pathway v1.2 - gene sets from pathway databases

Gene Expression

• MGI Expression Detected v1.2 - genes detected as expressed in data with a focus on gene expression during mouse development
• MSigDB Perturbation v1.2 - gene sets that change their expression after genetic and chemical perturbations

Regulatory Motifs

• Transcription Factor Targets v1.2 - genes identified by a transcription factor ChIP-chip experiment
• MSigDB Predicted Promoter Motifs v1.2 - gene sets that share a transcription factor binding motif
• MSigDB miRNA Motifs v1.2 - gene sets that share a 3'-UTR microRNA binding motif
• miRNA Targets v1.2 - genes that are downregulated in a microRNA overexpression experiment

Gene Families

• InterPro v1.2 - protein domains, families and functional sites
• TreeFam v1.2 - gene families of paralogs
• HGNC Gene Families v1.2 - gene sets based on sequence similarity, data from the literature, and manual curation