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A Common Language for Annotation of Genes from
Yeast, Flies and Mice
The Gene Ontologies
…and Plants and Worms
…and Humans
…and anything else!
Gene Ontology Objectives
• GO represents concepts used to classify specific parts of our biological knowledge:– Biological Process– Molecular Function– Cellular Component
• GO develops a common language applicable to any organism
• GO terms can be used to annotate gene products from any species, allowing comparison of information across species
Expansion of Sequence Info
Eukaryotic Genome Sequences Year Genome # GenesSize (Mb)
Yeast (S. cerevisiae) 1996 12 6,000
Worm (C. elegans) 1998 97 19,100
Fly (D. melanogaster) 2000 120 13,600
Plant (A. thaliana) 2001 125 25,500
Human (H. sapiens, 1st Draft) 2001 ~3000 ~35,000
Entering the Genome Sequencing Era
Baldauf et al. (2000)Science 290:972
MCM3
MCM2
CDC46/MCM5
CDC47/MCM7
CDC54/MCM4
MCM6
These proteins form a hexamer in the species that have been examined
Comparison of sequences from 4 organisms
http://www.geneontology.org/
Outline of Topics
• Introduction to the Gene Ontologies (GO)
• Annotations to GO terms
• GO Tools
• Applications of GO
What is an Ontology? (from OED)
1721 BAILEY, Ontology, an Account of being in the Abstract. 1733 (title) A Brief Scheme of Ontology or the Science of Being in General. a1832 BENTHAM Fragm. Ontol. Wks. 1843 VIII. 195 The field of ontology, or as it may otherwise be termed, the field of supremely abstract entities, is a yet untrodden labyrinth. 1884 BOSANQUET tr. Lotze's Metaph. 22 Ontology..as a doctrine of the being and relations of all reality, had precedence given to it over Cosmology and Psychology, the two branches of enquiry which follow the reality into its opposite distinctive forms.
Sriniga Srinivasan, Chief Ontologist, Yahoo!
The ontology. Dividing human knowledge into a clean set of categories is a lot like trying to figure out where to find that suspenseful black comedy at your corner video store. Questions inevitably come up, like are Movies part of Art or Entertainment? (Yahoo! lists them under the latter.) -Wired Magazine, May 1996
• Molecular Function = elemental activity/task– the tasks performed by individual gene products; examples are carbohydrate
binding and ATPase activity
• Biological Process = biological goal or objective– broad biological goals, such as mitosis or purine metabolism, that are accomplished
by ordered assemblies of molecular functions
• Cellular Component = location or complex– subcellular structures, locations, and macromolecular complexes; examples include
nucleus, telomere, and RNA polymerase II holoenzyme
The 3 Gene Ontologies
Function (what) Process (why)
Drive nail (into wood) Carpentry
Drive stake (into soil) Gardening
Smash roach Pest Control
Clown’s juggling object Entertainment
Example: Gene Product = hammer
Biological ExamplesMolecular FunctionMolecular FunctionBiological ProcessBiological Process Cellular ComponentCellular Component
term: MAPKKK cascade (mating sensu Saccharomyces)
goid: GO:0007244
definition: OBSOLETE. MAPKKK cascade involved in transduction of mating pheromone signal, as described in Saccharomyces.
definition_reference: PMID:9561267
comment: This term was made obsolete because it is a gene product specific term. To update annotations, use the biological process term 'signal transduction during conjugation with cellular fusion ; GO:0000750'.
Terms, Definitions, IDs
definition: MAPKKK cascade involved in transduction of mating pheromone signal, as described in Saccharomyces
Directed Cyclic Graph
Figure 4.1. Life cycles of heterothallic and homothallic strains of S. cerevisiae. Heterothallic strains can be stably maintained as diploids and haploids, whereas homothallic strains are stable only as diploids, because the transient haploid cells switch their mating type, and mate.
An Introduction to the Genetics and Molecular Biology of the Yeast Saccharomyces cerevisiae Fred Sherman 2000; Modified from: F. Sherman, Yeast genetics. The Encyclopedia of Molecular Biology and Molecular Medicine, pp. 302-325, Vol. 6. Edited by R. A. Meyers, VCH Pub., Weinheim, Germany,1997.
Nucleus
Nucleoplasm Nuclearenvelope
Chromosome Perinuclear spaceNucleolus
A child is a subset ofa parent’s elements
The cell component term Nucleus has 5 children
Parent-Child Relationships
Derivation of Romance languages from Latin. From R.A. Hall Jr., Introductory Linguistics; originally published by Chilton Books,now distributed by Rand McNally & Co.
“Tree” Relationships
Ontology RelationshipsDirected Acyclic Graph
http://www.ebi.ac.uk/ego
Evidence Codes for GO Evidence Codes for GO AnnotationsAnnotations
http://www.geneontology.org/doc/GO.evidence.html
IEA Inferred from Electronic Annotation
ISS Inferred from Sequence Similarity
IEP Inferred from Expression Pattern
IMP Inferred from Mutant Phenotype
IGI Inferred from Genetic Interaction
IPI Inferred from Physical Interaction
IDA Inferred from Direct Assay
RCA Inferred from Reviewed Computational Analysis
TAS Traceable Author Statement
NAS Non-traceable Author Statement
IC Inferred by Curator
ND No biological Data available
IEAInferred from Electronic Annotation
• Sequence Similarity (BLAST)
• Automatic transfer from mappings (InterPro2GO, EC2GO etc.)
-> Not manually reviewed
ISSInferred from Sequence or Structural
Similarity
• Sequence similarity
• Recognized domains
• Structural similarity
->Use of ‘with’ column recommended
IEPInferred from Expression Pattern
• Transcript levels (Northerns, microarrays)
• Protein levels (Western blots)
->Timing or localization of expression
->Biological process annotations
IMPInferred from Mutant Phenotype
• Gene mutation/knockout
• Overexpression/ectopic expression
• Anti-sense experiments
• RNAi experiments
• Specific protein inhibitors
IGIInferred from Genetic Interaction
• Suppressors, synthetic lethals…
• Functional complementation
• Rescue experiments
->Use of ‘with’ column recommended
IPIInferred from Physical Interaction
• 2-hybrid interactions
• Co-purification
• Co-immunoprecipitation
• Ion/complex/protein binding experiments
->Use of ‘with’ column recommended
IDAInferred from Direct Assay
• Enzyme assays
• In vitro reconstitution (e.g. transcription)
• Immunofluorescence (for cell. comp.)
• Cell fractionation (for cell. comp.)
• Physical interaction/binding assay
RCAInferred from Reviewed Computational
Analysis
• Non-sequence-based computational methods
• Genome-wide analyses (e.g. 2-hybrid)
• Combinations of large-scale experiments
TASTraceable Author Statement
• Support from review article
• Textbook ‘common knowledge’
->Data that can be ‘traced’ back
NASNon-traceable Author Statement
• Database entries that don't cite a paper
->Data that cannot be ‘traced’ back
ICInferred by Curator
• Not supported by any direct evidence
• Inferred from other GO annotations
-> GO term in ‘with/from’ column required
NDNo biological Data available
• molecular function unknown GO:0005554
• biological process unknown GO:0000004
• cellular component unknown GO:0008372
Curator found no information supporting any annotation
TAS/IDA
IMP/IGI/IPI
ISS/IEP
NAS
IEA
Term Hierarchy
Qualifiers
NOT: explicit note that a gene product is not associated with a GO term
colocalizes_with: only transient localization,or low resolution of an assay
contributes_to: gene product that is part of a complex can be annotated to the process/function of the complex
http://www.geneontology.org/GO.annotation.shtml#qual
The qualifier modifies the interpretation of a GO term
http://www.geneontology.org/doc/GO.evidence.html