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Bioinformatics Advance Access published online on March 9, 2006
Bioinformatics, 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
Received October 25, 2005
Revised February 9, 2006
Accepted March 4, 2006

Article

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

Gaëlle Lelandais 1 *, Pierre Vincens 2, Anne Badel-Chagnon 2, Stéphane Vialette 3, Claude Jacq 4, and Serge Hazout 2

1 Laboratoire de Génétique Moléculaire, CNRS UMR 8541, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris cedex 05, France; Equipe de Bioinformatique Génomique et Moléculaire, INSERM U726, Université Paris 7, case 7113, 2 Place Jussieu, 75251 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
4 Laboratoire de Génétique Moléculaire, CNRS UMR 8541, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris cedex 05, France

* To whom correspondence should be addressed.
Gaëlle Lelandais, E-mail: lelandais{at}biologie.ens.fr


  Abstract

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 Multidimensional Scaling (MDS) techniques, to compare the conformation of two gene expression networks, represented in a multi-dimensional space. The expression networks are optimally superimposed, taken into account two criteria: (1) inter-organism orthologous gene pairs have to be nearby points in the final multi-dimensional space, (2) the distortion of the gene expression networks, the organisation 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 and supplementary data can be found online at: http://www.biologie.ens.fr/lgmgml/publication/comp3d/.

Associate Editor: David Rocke
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