Ontology: a collection of terms and their definitions and the logical relationships between them
Gene Ontology (GO): a collection of terms and their definitions and the logical relationships between them describing gene products
nucleus “A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.” GO:0005634
molecular function “Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.”
biological process “Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.”
biological process examples: para-aminobenzoic acid biosynthetic process protein localization establishment of blood-nerve barrier circadian rhythm posterior midgut development
geneontology.org download mappings from other databases enzyme functions (EC, KEGG, MetaCyc) protein domains (Pfam, SMART, PRINTS,…) other controlled vocabularies of functions (E. coli functions, MIPS FunCat)
geneontology.org download annotations for various genomes
NCBI_NP NP_354299.2 lolD GO:0043190 ISS "ABC transporter, nucleotide binding/ATPase protein (lipoprotein)" taxon:176299 20070612 PAMGO_GAT geneontology.org download annotations for various genomes database gene product ID gene symbol GO term ID evidence code
evidence codes Allow curators to indicate the type of evidence for each gene-term annotation. experimental computational author statement e.g. IMPInferred from mutant phenotype IDAInferred from direct assay e.g. ISSInferred from sequence similarity IGCInferred from genome context e.g. TASTraceable author statement
NCBI_NP NP_354299.2 lolD GO:0043190 ISS "ABC transporter, nucleotide binding/ATPase protein (lipoprotein)" taxon:176299 20070612 PAMGO_GAT geneontology.org download annotations for various genomes database gene product ID gene symbol GO term ID evidence code description organism (taxon) ID date annotation project ID
geneontology.org repository of analysis tools that use GO search, edit and and browse ontologies / annotations software libraries statistical analysis text mining protein interactions enrichment analysis
significant expression change in a microarray experiment cluster from a protein interaction network some other experiment / analysis gene set whole genome (annotated) Which GO terms occur significantly more often than expected in this gene set? BiNGO GOstat ArrayTrack
Advantages of GO single set of terms to describe the function of gene products from all organisms. DAG structure provides a logical framework to represent knowledge at whatever level of detail is available. continually revised to reflect the state of current knowledge. can quantify strength of relationships between terms (semantic similarity). many statistical analysis tools available.
Limitations of GO GO is limited in scope: it does not cover processes that are not normal functions of gene products (e.g. oncogenesis). sequence attributes (e.g. introns/exons) protein structures or interactions evolution gene expression
Summary (1) The gene ontology (GO) is a structured, controlled vocabulary to describe the function of gene products. Terms in GO have logical relationships (“is a”, “part of”) with one another. Together these form a structure called a Directed Acyclic Graph (DAG). GO is formed of 3 separate ontologies describing different aspects of gene function: cellular component, molecular function and biological process.
Summary (2) geneontology.org is the central resource for downloading ontology, annotation and mapping files. evidence codes are used in annotations to show the experimental, computational or literature support for each function.
Summary (3) many software tools are available to support GO analysis of experimental data, including enrichment analysis by ArrayTrack (microarray expression data) BiNGO (protein interaction clusters) GOstat (any data in the form of gene sets)