Global similarity and local divergence in human and mouse gene co-expression networks

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dc.contributor.authorTsaparas, P.en
dc.contributor.authorMarino-Ramirez, L.en
dc.contributor.authorBodenreider, O.en
dc.contributor.authorKoonin, E. V.en
dc.contributor.authorJordan, I. K.en
dc.date.accessioned2015-11-24T17:01:24Z
dc.date.available2015-11-24T17:01:24Z
dc.identifier.issn1471-2148-
dc.identifier.urihttps://olympias.lib.uoi.gr/jspui/handle/123456789/10920
dc.rightsDefault Licence-
dc.subjectscale-free networksen
dc.subjectevolutionary dynamicsen
dc.subjectexpression profilesen
dc.subjectorthologous genesen
dc.subjectduplicate genesen
dc.subjectbiologyen
dc.subjecttranscriptomesen
dc.subjectconservationen
dc.subjectcoevolutionen
dc.subjectchimpanzeesen
dc.titleGlobal similarity and local divergence in human and mouse gene co-expression networksen
heal.abstractBackground: A genome-wide comparative analysis of human and mouse gene expression patterns was performed in order to evaluate the evolutionary divergence of mammalian gene expression. Tissue-specific expression profiles were analyzed for 9,105 human-mouse orthologous gene pairs across 28 tissues. Expression profiles were resolved into species-specific coexpression networks, and the topological properties of the networks were compared between species. Results: At the global level, the topological properties of the human and mouse gene coexpression networks are, essentially, identical. For instance, both networks have topologies with small-world and scale-free properties as well as closely similar average node degrees, clustering coefficients, and path lengths. However, the human and mouse coexpression networks are highly divergent at the local level: only a small fraction (< 10%) of coexpressed gene pair relationships are conserved between the two species. A series of controls for experimental and biological variance show that most of this divergence does not result from experimental noise. We further show that, while the expression divergence between species is genuinely rapid, expression does not evolve free from selective (functional) constraint. Indeed, the coexpression networks analyzed here are demonstrably functionally coherent as indicated by the functional similarity of coexpressed gene pairs, and this pattern is most pronounced in the conserved human-mouse intersection network. Numerous dense network clusters show evidence of dedicated functions, such as spermatogenesis and immune response, that are clearly consistent with the coherence of the expression patterns of their constituent gene members. Conclusion: The dissonance between global versus local network divergence suggests that the interspecies similarity of the global network properties is of limited biological significance, at best, and that the biologically relevant aspects of the architectures of gene coexpression are specific and particular, rather than universal. Nevertheless, there is substantial evolutionary conservation of the local network structure which is compatible with the notion that gene coexpression networks are subject to purifying selection.en
heal.accesscampus-
heal.fullTextAvailabilityTRUE-
heal.identifier.primaryDoi 10.1186/1471-2148-6-70-
heal.journalNameBmc Evolutionary Biologyen
heal.journalTypepeer reviewed-
heal.languageen-
heal.publicationDate2006-
heal.recordProviderΠανεπιστήμιο Ιωαννίνων. Σχολή Θετικών Επιστημών. Τμήμα Μηχανικών Ηλεκτρονικών Υπολογιστών και Πληροφορικήςel
heal.typejournalArticle-
heal.type.elΆρθρο Περιοδικούel
heal.type.enJournal articleen

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