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Bioinformatics Advance Access originally published online on March 9, 2006
Bioinformatics 2006 22(11):1359-1366; doi:10.1093/bioinformatics/btl087
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms

Gaëlle Lelandais 1,2,*, Pierre Vincens 2, Anne Badel-Chagnon 2, Stéphane Vialette 3, Claude Jacq 1 and Serge Hazout 2

1 Laboratoire de Génétique Moléculaire, CNRS UMR 8541, Ecole Normale Supérieure 46 rue d'Ulm, 75230 Paris cedex 05, France
2 Equipe de Bioinformatique Génomique et Moléculaire, INSERM U726, Université Paris 7 case 7113, 2 Place Jussieu, 75251 Paris cedex 05, France
3 Laboratoire de Recherche en Informatique, UMR CNRS 8623, Faculté des Sciences d'Orsay, Université Paris Sud 91405 Orsay, France

*To whom correspondence should be addressed.

Motivation: Molecular evolution, which is classically assessed by comparison of individual proteins or genes between species, can now be studied by comparing co-expressed functional groups of genes. This approach, which better reflects the functional constraints on the evolution of organisms, can exploit the large amount of data generated by genome-wide expression analyses. However, it requires new methodologies to represent the data in a more accessible way for cross-species comparisons.

Results: In this work, we present an approach based on Multi-dimensional Scaling techniques, to compare the conformation of two gene expression networks, represented in a multi-dimensional space. The expression networks are optimally superimposed, taking into account two criteria: (1) inter-organism orthologous gene pairs have to be nearby points in the final multi-dimensional space and (2) the distortion of the gene expression networks, the organization of which reflects the similarities between the gene expression measurements, has to be circumscribed. Using this approach, we compared the transcriptional programs that drive sporulation in budding and fission yeasts, extracting some common properties and differences between the two species.

Availability: The source code is freely distributed to academic users upon request to the authors. More information can be found online at http://www.biologie.ens.fr/lgmgml/publication/comp3d/.

Contact: lelandais{at}biologie.ens.fr

Supplementary information: Supplementary data are available at http://www.biologie.ens.fr/lgmgml/publication/comp3d/SupData.php

Received on October 25, 2005; revised on February 9, 2006; accepted on March 4, 2006

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