1. www. GeneOntology.org Gene Ontology Collaboration

2. 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.

3. Collaborating Projects FlyBase (UC, Berkeley; Univ. Cambridge) MGI (Jackson Labs, Bar Harbor, Maine) SGD (Stanford Univ.) TAIR (Carnegie Institution) WormDB (Cal Tech)

4. 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.

5. 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.

6. GO = Three Ontologies Biological Process = goal or objective within cell Molecular Function = elemental activity or task Cellular Component = location or complex

7. mouse fly yeast Gene Product Associations to an Ontology GO ID DB ID Evidence code Reference Citation NOT ID Term Definition Ontology Synonyms Is-a| Part-of Node1 ID Node2 ID

8. Yeast Microarray Results Yeast Microarray Results Assignment 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

9. FUNCTION voltage-gated ion channel xylulokinase succinate dehydrogenase NADH dehydrogenase ubiquinol--cytochrome-c reductase cytochrome-c oxidase Rieske Fe-S protein cytochrome-c oxidase cytochrome-c1 ubiquinol--cytochrome-c reductase succinate dehydrogenase subunit malate dehydrogenase ubiquinol--cytochrome-c reductase cytochrome-c1 acetyl-CoA hydrolase Annotating Microarray Clusters with GO

10. PROCESS other anion transport xylulose metabolism tricarboxylic acid cycle oxidative phosphorylation electron transport oxidative phosphorylation electron transport oxidative phosphorylation electron transport tricarboxylic acid cycle & electron transport tricarboxylic acid cycle electron transport acetyl-CoA metabolism Annotating Microarray Clusters with GO

11. Conservation of Worm and Yeast Sequences Classification of Sequence Groups by Process Chervitz et al., (1998) Science 282:2022-2028 Protein folding & degradation 13% Transport & Secretion 11% Unclassified 8% Signal transduction 11% Intermediary metabolism 28% Cytoskeletal 5% Ribosomal proteins 6% DNA/RNA metabolism 18% 1.2 1.5 1.1 1.0 0.6 2.1

12. Process Ontology: Mating developmental processescell-cell fusion mating (yeast) pheromone response transcription regulation karyogamy shmooing nuclear congression nuclear fusion establishment of cell polarity actin cytoskeleton reorganization pheromone induction of gene expression cell cycle arrest parent child budding

13. Process Ontology: Mating developmental processescell-cell fusion mating (yeast) conjugation (yeast) agglutination protein modification pheromone response cell cycle transcription regulation karyogamy shmooing nuclear congression microtubule-based movement microtubule depolymerization nuclear fusion establishment of cell polarity actin cytoskeleton reorganization intracellular protein traffic cell wall organization and biogenesis signal transduction cytoskeleton organization and biogenesis alpha-factor processing a-factor export alpha-factor maturation pheromone degradation pheromone processing pheromone induction of gene expression cell cycle arrest transduction of mating signal MAPKKK cascade adaptation to mating signal parent child microtubule function budding FIG1 OPY1 FIG2 PEA2 STE6 AGA1 AGA2 SAG1 KAR3 CIK1 TUB2 BIK1 STE26 STE13 KAR2 SEC63 KAR5 SEC72 SRM1 AKR1 STE50 MSN5 STE7 STE11 STE5 STE12

14. http://www.geneontology.org

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

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

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

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

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

30. Suzanna Lewis Chris Mungall John Richter Software from UC Berkeley & Berkeley Drosophila Genome Project

32. www. GeneOntology.org