www.GeneOntology.org

Gene Ontology Gene Ontology Collaboration Collaboration

• Objectives of the project• Plan and Method• Features of member sites

– GO Browser, BDGP– SGD– FlyBase– MGI

• Open Source! Web & FTP sites for data and software.

Collaborating Projects

• FlyBase (UC, Berkeley; Univ. Cambridge)

• MGI (Jackson Labs, Bar Harbor, Maine)

• SGD (Stanford Univ.)

• TAIR (Carnegie Institution)

• WormDB (Cal Tech)

Knowledge of the biological role of proteins in one organism can often be transferred to other organisms.

The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.

GO Objectives

Provide a controlled vocabulary for the description of third independent “ontologies”: molecular function and cellular component of gene products, as well as the biological process representing the gene product’s higher order role.

Use these terms as attributes of gene products in the collaborating databases. (gene product associations).

Allow queries across databases using GO terms, providing linkage of biological information across species, maintain history and dynamic linkage.

GO = Three OntologiesGO = Three Ontologies

• Biological Process = goal or objective within cell

• Molecular Function = elemental activity or

task

• Cellular Component = location or complex

mouse

fly

yeast

Gene Product Associations to an Ontology

GO IDDB IDEvidence codeReference CitationNOT

IDTermDefinitionOntologySynonyms

Is-a| Part-ofNode1 IDNode2 ID

Yeast Microarray ResultsYeast Microarray ResultsAssignment of Terms to Clusters

Microarray data from Figure 2 of Eisen et al. (1998). Cluster Analysis and display of genome-wide expression patterns, Proc. Natl. Acad. Sci. 95: 14863-14868

(F) mitochondrial ribosome

(G) ATP synthesis

(H) chromatin structure

(I) ribosome and translation

(J) DNA replication

FUNCTIONvoltage-gated ion channelxylulokinasesuccinate dehydrogenaseNADH dehydrogenaseubiquinol--cytochrome-c reductasecytochrome-c oxidaseRieske Fe-S proteincytochrome-c oxidasecytochrome-c1ubiquinol--cytochrome-c reductasesuccinate dehydrogenase subunitsuccinate dehydrogenase subunitsuccinate dehydrogenase subunitmalate dehydrogenaseubiquinol--cytochrome-c reductasecytochrome-c1acetyl-CoA hydrolase

Annotating Microarray Clusters with GOAnnotating Microarray Clusters with GO

PROCESSother anion transportxylulose metabolismtricarboxylic acid cycleoxidative phosphorylationelectron transportoxidative phosphorylationelectron transportoxidative phosphorylationelectron transportelectron transporttricarboxylic acid cycle & electron transporttricarboxylic acid cycle & electron transporttricarboxylic acid cycle & electron transporttricarboxylic acid cycleelectron transportelectron transportacetyl-CoA metabolism

Annotating Microarray Clusters with GOAnnotating Microarray Clusters with GO

Conservation of Worm and Yeast SequencesConservation of Worm and Yeast SequencesClassification of Sequence Groups by ProcessClassification of Sequence Groups by Process

Chervitz et al., (1998) Chervitz et al., (1998) ScienceScience 282:2022-2028 282:2022-2028

Protein folding &degradation

13%Transport &Secretion

11%

Unclassified8%

Signaltransduction

11%

Intermediarymetabolism

28%

Cytoskeletal5% Ribosomal

proteins6%

DNA/RNAmetabolism

18%

1.2

1.2

1.5

1.1

1.0 1.0

0.62.1

Process Ontology: MatingProcess Ontology: Matingdevelopmental processes cell-cell fusion

mating

(yeast)

pheromone response

transcription regulation

karyogamyshmooingnuclear congression

nuclear fusion

establishment of cell polarityactin cytoskeleton reorganization

pheromone induction of gene expressioncell cycle arrest

parent

child

budding

Process Ontology: MatingProcess Ontology: Matingdevelopmental processes cell-cell fusion

mating(yeast) conjugation

(yeast)

agglutinationprotein modification

pheromone response

cell cycletranscription regulation

karyogamyshmooing

nuclear congression

microtubule-based movementmicrotubule depolymerization

nuclear fusion

establishment of cell polarityactin cytoskeleton reorganizationintracellular protein trafficcell wall organization and biogenesis

signal transduction

cytoskeleton organizationand biogenesis

alpha-factor processinga-factor exportalpha-factor maturationpheromone degradation

pheromoneprocessing

pheromone induction of gene expressioncell cycle arresttransduction of mating signal

MAPKKK cascadeadaptation to mating signal

parent

child

microtubule function

budding

FIG1 OPY1FIG2 PEA2

STE6

AGA1 AGA2 SAG1

KAR3 CIK1 TUB2 BIK1

STE26

STE13

KAR2 SEC63 KAR5 SEC72

SRM1 AKR1 STE50 MSN5

STE7 STE11 STE5

STE12

http://www.geneontology.org

ftp://genome-ftp.stanford.edu/pub/go

http://www.fruitfly.org/annot/go/

http://genome-www.stanford.edu/Saccharomyces/

http://flybase.bio.indiana.edu/

http://www.informatics.jax.org/

Suzanna Lewis

Chris Mungall

John Richter

Software from UC Berkeley & Berkeley Drosophila Genome

Project

www.GeneOntology.org