Yeast transcriptional regulatory network

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Yeast transcriptional regulatory network
metabolic network

• Tony
• 28/09/2004

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Transcriptional regulatory code of a eukaryotic
genome

• Richard A. Young, et al. (2004) Nature 431,
  99-104.

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Summary of the work

• This work presents mainly some novel experimental
  results. Probably for the first time to date, the
  transcriptional regulatory code is deciphered
  genome-widely.
• The genome-scale TR code
• Simple analysis of the code

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TR code of yeast genome

• Genome-wide location analysis
• Integration of genome-wide location data,
  phylogenetically conserved sequences, and prior
  knowledge.
• The code

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Simple statistics of the code

• The distribution of the binding sites for
  transcriptional regulators
• Promoter architectures
• Single regulator
• Repetitive motifs
• Multiple regulators
• Co-occurring regulators
• Environment-dependent binding behaviors
• Condition-invariant
• Condition-enabled
• Condition-expanded
• Condition-altered

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Global organization of metabolic fluxes in the
bacterium Escherichia coli

• A.-L. Barabasi, et al. (2004) Nature 427, 839-842.

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Summary of the work

• This paper utilizes FBA techniques to study the
  metabolic fluxes in the yeast metabolic network.
• The paper has two major conclusions
• The flux distribution is scale free.
• The existence of High-flux backbone (HFB).

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Flux distribution

• Flux Balance Analysis (FBA)
• Flux distribution is scale free, independent of
  the environmental conditions and regardless of
  whether its optimized for maximal growth rate or
  not.
• These findings imply that the observed flux
  distribution is a generic feature of flux
  conservation on a scale-free network.

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High-flux backbone

• The local flux is inhomogenous.
• High-flux backbone (HFB)
• Only the reactions in the HFB undergo noticeable
  flux change when conditions change.