title: On cycles in the transcription network of Saccharomyces cerevisiae.
abstract: BACKGROUND
  We investigate the cycles in the transcription network of Saccharomyces cerevisiae. Unlike a similar network of Escherichia coli, it contains many cycles. We characterize properties of these cycles and their place in the regulatory mechanism of the cell.
  
  
  RESULTS
  Almost all cycles in the transcription network of Saccharomyces cerevisiae are contained in a single strongly connected component, which we call LSCC (L for "largest"), except for a single cycle of two transcription factors. The fact that LSCC includes almost all cycles is well explained by the properties of a random graph with the same in- and out-degrees of the nodes. Among different physiological conditions, cell cycle has the most significant relationship with LSCC, as the set of 64 transcription interactions that are active in all phases of the cell cycle has overlap of 27 with the interactions of LSCC (of which there are 49).Conversely, if we remove the interactions that are active in all phases of the cell cycle (25% of interactions to transcription factors), the LSCC would have only three nodes and 5 edges, many fewer than expected. This subgraph of the transcription network consists mostly of interactions that are active only in the stress response subnetwork. We also characterize the role of LSCC in the topology of the network. We show that LSCC can be used to define a natural hierarchy in the network and that in every physiological subnetwork LSCC plays a pivotal role.
  
  
  CONCLUSIONS
  Apart from those well-defined conditions, the transcription network of Saccharomyces cerevisiae is devoid of cycles. It was observed that two conditions that were studied and that have no cycles of their own are exogenous: diauxic shift and DNA repair, while cell cycle and sporulation are endogenous. We claim that in a certain sense (slow recovery) stress response is endogenous as well.
authors.affiliation: Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA. jijeong@cse.psu.edu
authors.forename: Jieun
authors.initials: J
authors.lastname: Jeong
authors.forename: Piotr
authors.initials: P
authors.lastname: Berman
mesh_terms: D000465:Algorithms; D002453:Cell Cycle / Q000235:genetics; D025461:Feedback, Physiological / Q000235:genetics; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D006801:Humans; D008954:Models, Biological; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors