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


CONCLUSIONS
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.
Farkas
Illés J
IJ
Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15261, USA. illes.farkas@gmail.com <illes.farkas@gmail.com>
Wu
Chuang
C
Chennubhotla
Chakra
C
Bahar
Ivet
I
Oltvai
Zoltán N
ZN
D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D030541:Databases, Genetic; D019143:Evolution, Molecular; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D012984:Software; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors