title: Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae.
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.
  
  
  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.
authors.affiliation: Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15261, USA. illes.farkas@gmail.com <illes.farkas@gmail.com>
authors.forename: Illés J
authors.initials: IJ
authors.lastname: Farkas
authors.forename: Chuang
authors.initials: C
authors.lastname: Wu
authors.forename: Chakra
authors.initials: C
authors.lastname: Chennubhotla
authors.forename: Ivet
authors.initials: I
authors.lastname: Bahar
authors.forename: Zoltán N
authors.initials: ZN
authors.lastname: Oltvai
mesh_terms: 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
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors