Abstract
Ontologies are fundamental knowledge representations that provide not only standards for annotating and indexing biological information, but also the basis for implementing functional classification and interpretation models. This chapter discusses the application of gene ontology (GO) for predictive tasks in functional genomics. It focuses on the problem of analyzing functional patterns associated with gene products. This chapter is divided into two main parts. The first part overviews GO and its applications for the development of functional classification models. The second part presents two methods for the characterization of genomic information using GO. It discusses methods for measuring functional similarity of gene products, and a tool for supporting gene expression clustering analysis and validation.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
The Gene Ontology Consortium. (2001) Creating the gene ontology resource: design and implementation. Genome Res. 11, 1425–1433.
Ouzounis, C., Coulson, R., Enright, A., Kunin, V., and Pereira-Leal, J. (2003) Classification schemes for protein structure and function. Nat. Rev. Genet. 4, 508–519.
Harris, M. and Parkinson, H. (2003) Standards and ontologies for functional genomics: towards unified ontologies for biology and biomedicine. Compar. Funct. Genomics 4, 116–120.
Bard, J. (2003) Ontologies: formalising biological knowledge for bioinformatics. BioEssays 25, 501–506.
King, O., Lee, J., Dudley, A., Jansen, D., Church, G., and Roth, F. (2003) Predicting phenotype from patterns of annotation. Bioinformatics 19(Suppl. 1), 183–189.
Hvidsten, T., Laegreid, A., and Komorowski, J. (2003) Learning rule-based models of biological process from gene expression time profiles using Gene Ontology. Bioinformatics 19, 1116–1123.
King, O., Foulger, R., Dwight, S., White, J., and Roth, F. (2003) Predicting gene function from patterns of annotation. Genome Res. 13, 896–904.
Laegreid, A., Hvidsten, T., Midelfart, H., Komorowski, J., and Sandvik, A. (2003) Predicting gene ontology biological process from temporal gene expression patterns. Genome Res. 13, 965–979.
Iyer, V., Eisen, M., Ross, D., et al. (1999) The transcriptional program in the response of human fibroblast to serum. Science 283, 83–87.
Zhong, J., Zhu, H., Li, Y., and Yu, Y. (2002) Conceptual graph matching for semantic search, in Conceptual Structures: Integration and Interfaces (Priss, U., Corbett, D., and Angelova, G., eds.), Springer Verlag, London, UK, pp. 92–106.
Budanitsky, A. and Hirst, G. (2001) Semantic distance in WordNet: an experimental, application-oriented evaluation of five measures, in Workshop on WordNet and Other Lexical Resources, Pittsburgh.
Resnik, P. (1995) Using information content to evaluate semantic similarity in a taxonomy, in Proceedings of the 14th International Joint Conference on Artificial Intelligence, Montreal, Canada (Mellish, C. S., ed.), Morgan Kaufman, San Mateo, CA, pp. 448–453.
Lin, D. (1998) An information-theoretic definition of similarity, in Proceedings of the 15th International Conference on Machine Learning, Montreal, Canada (Mellish, C. S., ed.), Morgan Kaufman, San Mateo, CA, pp. 296–304.
Lord, P., Stevens, R., Brass, A., and Goble, C. (2003) Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19, 1275–1283.
Cho, R., Campbell, M., Winzeler, E., et al. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2, 65–73.
Al-Shahrour, F., Diaz-Uriarte, R., and Dopazo, J. (2003) FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20, 578–580 (epub).
Khatri, P., Draghici, S., Ostermeier, G. C., and Krawetz, S. A. (2002) Profiling gene expression using onto-express. Genomics 79, 1–5.
Doniger, S. W., Salomonis, N., Dahlquist, K. D., Vranizan, K., Lawlor, S. C., and Conklin, B. R. (2003) MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol. 4, R7.
Robinson, M. D., Grigull, J., Mohammad, N., and Hughes, T. R. (2002) FunSpect: a web-based cluster interpreter for yeast. BMC Bioinformatics 3, 1–5.
Zeeberg, B. R., Feng, W., Wang, G., et al. (2003) GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol. 4(4), R28.1–R28.8.
Mateos, A., Herrero, J., Tamames, J., and Dopazo, J. (2002) Supervised neural networks for clustering conditions in DNA array data after reducing noise by clustering gene expression profiles, in Methods of Microarray Data Analysis II (Lin, S. and Johnson, K., eds.), Kluwer, Boston, MA.
Slonim, D. K. (2002) From patterns to pathways: gene expression data analysis comes of age. Nat. Genet. (Suppl. The Chipping Forecast) 32, 502–508.
Westfall, P. H. and Young, S. S. (1993) Resampling-Based Multiple Testing, John Wiley & Sons, New York.
Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57, 289–300.
Benjamini, Y. and Yekutieli, D. (2001) The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 29, 1165–1188.
Eisen, M., Spellman, P. L., Brown, P. O., and Botsein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14,863–14,868.
Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botsein, D., Brown, P. O., and Herskowitz, I. (1998) The transcriptional program sporulation in budding yeast. Science 282, 699–705.
Herrero, J., Valencia, A., and Dopazo, J. (2001) A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics 17, 126–136.
Herrero, J., Al-Shahrour, F., Diaz-Uriarte, R., et al. (2003) GEPAS, a web-based resource for microarray gene expression data analysis. Nucleic Acids Res. 31, 3461–3467.
Pritchard, C. C., Hsu, L., and Nelson, P. S. (2001) Project normal: defining normal variance in mouse gene expression. Proc. Natl. Acad. Sci. USA 98, 13,266–13,271.
Diaz-Uriarte, R., Al-Shahrour, F., and Dopazo, J. (2003) Use of GO terms to understand the biological significance of microarray differential gene expression data, in Methods of Microarray Data Analysis III (Lin, S. and Johnson, K., eds.), Kluwer, Boston, MA; in press.
Mota, V. K., Lindgren, C. M., Eriksson, K. F., et al. (2003) PGC-1-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 34, 267–273.
Acknowledgment
We thank Oliver Bodenreider for helpful advice on ontologies. This work was supported by grant BIO2001-0068 from the Ministerio de Ciencia y Tecnología. F.A. was partly supported by a visiting fellowship from the US National Library of Medicine.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Humana Press Inc.
About this protocol
Cite this protocol
Azuaje, F., Al-Shahrour, F., Dopazo, J. (2006). Ontology-Driven Approaches to Analyzing Data in Functional Genomics. In: Larson, R.S. (eds) Bioinformatics and Drug Discovery. Methods in Molecular Biology, vol 316. Humana Press. https://doi.org/10.1385/1-59259-964-8:67
Download citation
DOI: https://doi.org/10.1385/1-59259-964-8:67
Publisher Name: Humana Press
Print ISBN: 978-1-58829-346-6
Online ISBN: 978-1-59259-964-6
eBook Packages: Springer Protocols