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GeneOntology

Gene Ontology Collaboration. www. GeneOntology .org. 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)

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GeneOntology

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  1. Gene Ontology Collaboration www.GeneOntology.org

  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”: molecularfunction and cellular component of gene products, as well as the biologicalprocess 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. Gene Product Associations to an Ontology yeast ID Term Definition Ontology Synonyms fly Is-a| Part-of Node1 ID Node2 ID GO ID DB ID Evidence code Reference Citation NOT mouse

  8. Yeast Microarray ResultsAssignment of Terms to Clusters (F) mitochondrial ribosome (G) ATP synthesis (H) chromatin structure (I) ribosome and translation (J) DNA replication 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

  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 succinate dehydrogenase subunit 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 electron transport tricarboxylic acid cycle & electron transport tricarboxylic acid cycle & electron transport tricarboxylic acid cycle & electron transport tricarboxylic acid cycle electron transport electron transport acetyl-CoA metabolism Annotating Microarray Clusters with GO

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

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

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

  14. http://www.geneontology.org

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

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

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

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

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

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

  21. www.GeneOntology.org

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