(1) Laboratoire de Genetique Moleculaire, CNRS UMR 8541, Ecole Normale Superieure, 46 rue d'Ulm, 75230 Paris cedex 05, France.

(2) Equipe de Bioinformatique Genomique et Moleculaire, INSERM U726, Universite Paris 7, case 7113, 2 Place Jussieu, 75251 Paris cedex 05, France.

(3) Laboratoire de Recherche en Informatique, UMR CNRS 8623, Faculte des Sciences d'Orsay, Universite Paris Sud, 91405 Orsay, France.

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 overall, genome-wide expression analyses. However, it requires new methodologies to represent the data in a more accessible way for cross-species comparisons. 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.