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