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 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 ID DB ID Evidence code Reference Citation NOT ID Term Definition Ontology Synonyms Is-a| Part-of Node1 ID Node2 ID
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: (F) mitochondrial ribosome (G) ATP synthesis (H) chromatin structure (I) ribosome and translation (J) DNA replication
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
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
Conservation of Worm and Yeast Sequences Classification of Sequence Groups by Process Chervitz et al., (1998) Science 282: Protein folding & degradation 13% Transport & Secretion 11% Unclassified 8% Signal transduction 11% Intermediary metabolism 28% Cytoskeletal 5% Ribosomal proteins 6% DNA/RNA metabolism 18%