Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: Motivation: Molecular evolution, which is classically assessed by comparison of individual proteins or genes beten 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. Hover, it requires new methodologies to represent the data in a more accessible way for cross-species comparisons.#R##N##R##N#Results: In this work,  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 beten the gene expression measurements, has to be circumscribed. Using this approach,  compared the transcriptional programs that drive sporulation in budding and fission yeasts, extracting some common properties and differences beten the two species.#R##N##R##N#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/.#R##N##R##N#Contact: lelandais@biologie.ens.fr#R##N##R##N#Supplementary information: Supplementary data are available at http://www.biologie.ens.fr/lgmgml/publication/comp3d/SupData.php
['Gaëlle Lelandais', 'Pierre Vincens', 'Anne Badel-Chagnon', 'Stéphane Vialette', 'Claude Jacq', 'S. Hazout']
I am writing a research paper on a idea Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms
[{"from": "human", "value": "I am writing a research paper on a idea Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms"}, {"from": "gpt", "value": "Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: Motivation: Molecular evolution, which is classically assessed by comparison of individual proteins or genes beten 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. Hover, it requires new methodologies to represent the data in a more accessible way for cross-species comparisons.#R##N##R##N#Results: In this work,  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 beten the gene expression measurements, has to be circumscribed. Using this approach,  compared the transcriptional programs that drive sporulation in budding and fission yeasts, extracting some common properties and differences beten the two species.#R##N##R##N#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/.#R##N##R##N#Contact: lelandais@biologie.ens.fr#R##N##R##N#Supplementary information: Supplementary data are available at http://www.biologie.ens.fr/lgmgml/publication/comp3d/SupData.php"}]