Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms
| Autor: | Pierre Vincens, Gaëlle Lelandais, Claude Jacq, S. Hazout, Stéphane Vialette, Anne Badel-Chagnon |
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| Přispěvatelé: | Régulation de l'expression génétique (REG), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Duponchelle, Martine |
| Rok vydání: | 2006 |
| Předmět: |
Statistics and Probability
Source code media_common.quotation_subject Saccharomyces cerevisiae Computational biology Space (commercial competition) Biology Biochemistry Evolution Molecular Fungal Proteins 03 medical and health sciences 0302 clinical medicine Species Specificity Molecular evolution Gene Expression Regulation Fungal Schizosaccharomyces Gene expression [SDV.BBM] Life Sciences [q-bio]/Biochemistry Molecular Biology [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology Molecular Biology Gene 030304 developmental biology media_common Genetics 0303 health sciences Genome Models Statistical Gene Expression Profiling Computational Biology Expression (mathematics) Computer Science Applications Computational Mathematics Computational Theory and Mathematics Multi dimensional Software 030217 neurology & neurosurgery Orthologous Gene |
| Zdroj: | Bioinformatics Bioinformatics, Oxford University Press (OUP), 2006, 22, pp.1359-1366 |
| ISSN: | 1367-4811 1367-4803 |
| DOI: | 10.1093/bioinformatics/btl087 |
| Popis: | 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 . Contact: lelandais@biologie.ens.fr Supplementary information: Supplementary data are available at |
| Databáze: | OpenAIRE |
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