Research article
Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae
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* Corresponding author: Zoltán N Oltvai oltvai@pitt.edu
- † Equal contributors
1 Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
2 Department of Biological Physics and HAS Group, Eötvös University, Budapest, 1117, Hungary
3 Department of Computational Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
BMC Bioinformatics 2006, 7:478 doi:10.1186/1471-2105-7-478
Published: 28 October 2006Abstract
Background
Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmental signals in the context of the cell's own internal state. However, the network topological basis of developing such integrated responses remains poorly understood.
Results
By studying the TR network of the yeast Saccharomyces cerevisiae we show that an intermediate layer of transcription factors naturally segregates into distinct subnetworks. In these topological units transcription factors are densely interlinked in a largely hierarchical manner and respond to external signals by utilizing a fraction of these subnets.
Conclusion
As transcriptional regulation represents the 'slow' component of overall information processing, the identified topology suggests a model in which successive waves of transcriptional regulation originating from distinct fractions of the TR network control robust integrated responses to complex stimuli.