Research article

Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae

Illés J Farkas^1,2* , Chuang Wu^3* , Chakra Chennubhotla³ , Ivet Bahar³ and Zoltán N Oltvai¹

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

author email corresponding author email* Contributed equally

BMC Bioinformatics 2006, 7:478doi:10.1186/1471-2105-7-478

Published:	28 October 2006

Abstract

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.