共查询到20条相似文献,搜索用时 15 毫秒
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Serial regulation of transcriptional regulators in the yeast cell cycle 总被引:44,自引:0,他引:44
Simon I Barnett J Hannett N Harbison CT Rinaldi NJ Volkert TL Wyrick JJ Zeitlinger J Gifford DK Jaakkola TS Young RA 《Cell》2001,106(6):697-708
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The topology of regulatory networks contains clues to their overall design principles and evolutionary history. We find that while in- and out-degrees of a given protein in the regulatory network are not correlated with each other, there exists a strong negative correlation between the out-degree of a regulatory protein and in-degrees of its targets. Such correlation positions large regulatory modules on the periphery of the network and makes them rather well separated from each other. We also address the question of relative importance of different classes of proteins quantified by the lethality of null-mutants lacking one of them as well as by the level of their evolutionary conservation. It was found that in the yeast regulatory network highly connected proteins are in fact less important than their low-connected counterparts. 相似文献
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Computational discovery of gene modules and regulatory networks 总被引:23,自引:0,他引:23
Bar-Joseph Z Gerber GK Lee TI Rinaldi NJ Yoo JY Robert F Gordon DB Fraenkel E Jaakkola TS Young RA Gifford DK 《Nature biotechnology》2003,21(11):1337-1342
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Intrinsic disorder in yeast transcriptional regulatory network 总被引:2,自引:0,他引:2
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A graph-based approach to systematically reconstruct human transcriptional regulatory modules 总被引:2,自引:0,他引:2
Yan X Mehan MR Huang Y Waterman MS Yu PS Zhou XJ 《Bioinformatics (Oxford, England)》2007,23(13):i577-i586
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Pierre R Bushel Nicholas A Heard Roee Gutman Liwen Liu Shyamal D Peddada Saumyadipta Pyne 《BMC systems biology》2009,3(1):93-21
Background
Fission yeast Schizosaccharomyces pombe and budding yeast Saccharomyces cerevisiae are among the original model organisms in the study of the cell-division cycle. Unlike budding yeast, no large-scale regulatory network has been constructed for fission yeast. It has only been partially characterized. As a result, important regulatory cascades in budding yeast have no known or complete counterpart in fission yeast. 相似文献14.
High-throughput biological data offer an unprecedented opportunity to fully characterize biological processes. However, how to extract meaningful biological information from these datasets is a significant challenge. Recently, pathway-based analysis has gained much progress in identifying biomarkers for some phenotypes. Nevertheless, these so-called pathway-based methods are mainly individual-gene-based or molecule-complex-based analyses. In this paper, we developed a novel module-based method to reveal causal or dependent relations between network modules and biological phenotypes by integrating both gene expression data and protein-protein interaction network. Specifically, we first formulated the identification problem of the responsive modules underlying biological phenotypes as a mathematical programming model by exploiting phenotype difference, which can also be viewed as a multi-classification problem. Then, we applied it to study cell-cycle process of budding yeast from microarray data based on our biological experiments, and identified important phenotype- and transition-based responsive modules for different stages of cell-cycle process. The resulting responsive modules provide new insight into the regulation mechanisms of cell-cycle process from a network viewpoint. Moreover, the identification of transition modules provides a new way to study dynamical processes at a functional module level. In particular, we found that the dysfunction of a well-known module and two new modules may directly result in cell cycle arresting at S phase. In addition to our biological experiments, the identified responsive modules were also validated by two independent datasets on budding yeast cell cycle. 相似文献
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