On cycles in the transcription network of Saccharomyces cerevisiae View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-01-31

AUTHORS

Jieun Jeong, Piotr Berman

ABSTRACT

BackgroundWe 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.ResultsAlmost 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.ConclusionApart 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. More... »

PAGES

12

References to SciGraph publications

  • 2002-08. NOBEL LECTURE: Yeast and Cancer in BIOSCIENCE REPORTS
  • 2004-09. Genomic analysis of regulatory network dynamics reveals large topological changes in NATURE
  • <error retrieving object. in <ERROR RETRIEVING OBJECT
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    http://scigraph.springernature.com/pub.10.1186/1752-0509-2-12

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    http://dx.doi.org/10.1186/1752-0509-2-12

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/18237406


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