Title: Restructuring the Gene Ontology to emphasise regulative pathways and to improve gene similarity queries

Authors: Alessia Visconti, Roberto Esposito, Francesca Cordero

Addresses: Department of Computer Science, University of Torino, Corso Svizzera 185, 10049, Torino, Italy. ' Department of Computer Science, University of Torino, Corso Svizzera 185, 10049, Torino, Italy. ' Department of Clinical and Biological Sciences, University of Torino, Regione Gonzole 10, 10043, Orbassano, Italy

Abstract: The Gene Ontology (GO) has been developed to provide a structured vocabulary for genes description. Conversely, gene functional similarity measures would benefit from a structure tailored to emphasise genes involved in the same biological context. Therefore, such measures often find it difficult to fully exploit the information in the GO. This paper reorganises the GO to emphasise regulative information thus providing a better structure for functional analysis. A gene functional similarity measure exploiting the new structure is proposed. Empirical evidence shows that the new structure correctly captures regulative processes and that it can be used to support the proposed measure.

Keywords: gene ontology structure; gene functional similarity; pathways analysis; computational biology; regulative pathways; gene similarity queries; gene descriptions; functional analysis.

DOI: 10.1504/IJCBDD.2011.041411

International Journal of Computational Biology and Drug Design, 2011 Vol.4 No.3, pp.220 - 238

Available online: 21 Jul 2011

Full-text access for editors Access for subscribers Purchase this article Comment on this article