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Bioinform Biol Insights. 2008 Jul 14;2:307-16.

Evidence of highly regulated genes (in-Hubs) in gene networks of Saccharomyces cerevisiae.

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Department of Medicine, The Computational Medicine Group, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Solna, SE-171 76 Stockholm, Sweden.


Uncovering interactions between genes, gene networks, is important to increase our understanding of intrinsic cellular processes and responses to external stimuli such as drugs. Gene networks can be computationally inferred from repeated measurements of gene expression, using algorithms, which assume that each gene is controlled by only a small number of other proteins. Here, by extending the transcription network with cofactors (defined from protein-protein binding data) as active regulators, we identified the effective gene network, providing evidence of in-hubs in the gene regulatory networks of yeast. Then, using the notion that in-hub genes will be differentially expressed over several experimental conditions, we designed an algorithm, the HubDetector, enabling identification of in-hubs directly from gene expression data. Applying the HubDetector to 488 genome-wide expression profiles from two independent datasets, we identified putative in-hubs overlapping significantly with in-hubs in the effective gene network.


algorithm; gene expression; in-hubs; network; protein-protein interactions; transcription regulation

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