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CLOE Identification of putative functional relationships among genes by comparison of expression profiles between two species.doc

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CLOE Identification of putative functional relationships among genes by comparison of expression profiles between two species

BMC Bioinformatics BioMedCentral Methodology article Open Access CLOE: Identification of putative functional relationships among genes by comparison of expression profiles between two species Maurizio Pellegrino1, Paolo Provero2, Lorenzo Silengo1 and Ferdinando Di Cunto*1 Address: 1Department of Genetics, Biology and Biochemistry, Via Santena 5 bis, 10126, Torino, Italy and 2Fondazione per le Biotecnologie, Viale Settimio Severo, Torino, Italy Email: Maurizio Pellegrino - pellegrino@; Paolo Provero - vero@; Lorenzo Silengo - lorenzo.silengo@unito.it; Ferdinando Di Cunto* - ferdinando.dicunto@unito.it * Corresponding author Published: 19 November 2004 Received: 11 August 2004 Accepted: 19 November 2004 BMC Bioinformatics 2004, 5:179 doi:10.1186/1471-2105-5-179 This article is available from: /1471-2105/5/179 ? 2004 Pellegrino et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Public repositories of microarray data contain an incredible amount of information that is potentially relevant to explore functional relationships among genes by meta-analysis of expression profiles. However, the widespread use of this resource by the scientific community is at the moment limited by the limited availability of effective tools of analysis. We here describe CLOE, a simple cDNA microarray data mining strategy based on meta-analysis of datasets from pairs of species. The method consists in ranking EST probes in the datasets of the two species according to the similarity of their expression profiles with that of two EST probes from orthologous genes, and extracting orthologous EST pairs from a given top interval of the ranked lists. The Gene Ontology annotation