{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,27]],"date-time":"2025-12-27T21:13:58Z","timestamp":1766870038198,"version":"build-2065373602"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: The source code is freely distributed to academic users upon request to the authors. More information can be found online at .<\/jats:p>\n               <jats:p>Contact: \u00a0lelandais@biologie.ens.fr<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl087","type":"journal-article","created":{"date-parts":[[2006,3,10]],"date-time":"2006-03-10T01:24:17Z","timestamp":1141953857000},"page":"1359-1366","source":"Crossref","is-referenced-by-count":13,"title":["Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms"],"prefix":"10.1093","volume":"22","author":[{"given":"Ga\u00eblle","family":"Lelandais","sequence":"first","affiliation":[{"name":"Laboratoire de G\u00e9n\u00e9tique Mol\u00e9culaire, CNRS UMR 8541, Ecole Normale Sup\u00e9rieure 1 \u00a0 1 \u00a0 \u00a0 46 rue d'Ulm, 75230 Paris cedex 05, France"},{"name":"Equipe de Bioinformatique G\u00e9nomique et Mol\u00e9culaire, INSERM U726, Universit\u00e9 Paris 7 2 \u00a0 2 \u00a0 \u00a0 case 7113, 2 Place Jussieu, 75251 Paris cedex 05, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre","family":"Vincens","sequence":"additional","affiliation":[{"name":"Equipe de Bioinformatique G\u00e9nomique et Mol\u00e9culaire, INSERM U726, Universit\u00e9 Paris 7 2 \u00a0 2 \u00a0 \u00a0 case 7113, 2 Place Jussieu, 75251 Paris cedex 05, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne","family":"Badel-Chagnon","sequence":"additional","affiliation":[{"name":"Equipe de Bioinformatique G\u00e9nomique et Mol\u00e9culaire, INSERM U726, Universit\u00e9 Paris 7 2 \u00a0 2 \u00a0 \u00a0 case 7113, 2 Place Jussieu, 75251 Paris cedex 05, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"St\u00e9phane","family":"Vialette","sequence":"additional","affiliation":[{"name":"Laboratoire de Recherche en Informatique, UMR CNRS 8623, Facult\u00e9 des Sciences d'Orsay, Universit\u00e9 Paris Sud 3 \u00a0 3 \u00a0 \u00a0 91405 Orsay, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claude","family":"Jacq","sequence":"additional","affiliation":[{"name":"Laboratoire de G\u00e9n\u00e9tique Mol\u00e9culaire, CNRS UMR 8541, Ecole Normale Sup\u00e9rieure 1 \u00a0 1 \u00a0 \u00a0 46 rue d'Ulm, 75230 Paris cedex 05, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Serge","family":"Hazout","sequence":"additional","affiliation":[{"name":"Equipe de Bioinformatique G\u00e9nomique et Mol\u00e9culaire, INSERM U726, Universit\u00e9 Paris 7 2 \u00a0 2 \u00a0 \u00a0 case 7113, 2 Place Jussieu, 75251 Paris cedex 05, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,3,9]]},"reference":[{"key":"2023012408400272700_b1","doi-asserted-by":"crossref","first-page":"3351","DOI":"10.1073\/pnas.0530258100","article-title":"Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms","volume":"100","author":"Alter","year":"2003","journal-title":"Proc. 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