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Gene network reconstruction from microarray data

TitleGene network reconstruction from microarray data
Publication TypeJournal Article
Year of Publication2009
AuthorsJaffrezic, F, Tosser-Klopp, G
JournalBMC Proceedings
Volume3, S4
Abstract

BackgroundOften, software available for biological pathways reconstruction rely on literature search to find links between genes. The aim of this study is to reconstruct gene networks from microarray data, using Graphical Gaussian models.ResultsThe GeneNet R package was applied to the Eadgene chicken infection data set. No significant edges were found for the list of differentially expressed genes between conditions MM8 and MA8. On the other hand, a large number of significant edges were found among 85 differentially expressed genes between conditions MM8 and MM24.ConclusionMany edges were inferred from the microarray data. Most of them could, however, not be validated using other pathway reconstruction software. This was partly due to the fact that a quite large proportion of the differentially expressed genes were not annotated. Further biological validation is therefore needed for these networks, using for example in vitro invalidation of genes.