By Uri Alon
Offers layout rules that govern the constitution and behaviour of organic networks similar to gene circuits, highlighting easy, ordinary circuit components that make up the community. This publication offers a quantitative concept for which circuits are present in a given surroundings and a mathematical framework for figuring out organic circuits.
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Extra resources for An Introduction to Systems Biology: Design Principles of Biological Circuits
Examine the simplest network motif in transcription networks, negative autoregulation. Show that this motif has useful functions: speeding up the response time of transcription interactions and stabilizing them. 2 Patter ns, Rand omized Netw or k s, and Netw or k Motifs The transcription network of E. coli contains numerous patterns of nodes and edges. Our approach will be to look for meaningful patterns on the basis of statistical significance. To define statistical significance, we compare the network to an ensemble of randomized networks.
MRNA dynamics. In the main text, we considered the activation of transcription of a gene (mRNA production) and used a dynamical equation to describe the changes in the concentration of the gene product, the protein Y. In this equation, dY/dt = b – α Y, the parameter b describes the rate of protein production. In reality, mRNA needs to be translated to form the protein, and mRNA itself is also degraded by specific enzymes. a. Derive dynamical equations for the rate of change of mRNA and the rate of change of the protein product, assuming that mRNA is produced at rate bm and degraded at rate αm, and that each mRNA produces on average p protein molecules over its lifetime.
For example, a function with several plateaus and thresholds was found in the lac system of E. 5) (See color insert following page 112). , 2002; Beer and Tavazoie, 2004). The functional form of input functions can be readily changed by means of mutations in the promoter of the regulated gene. , 2006). It appears that the precise form of the input function of each gene is under selection pressure during evolution. 5 (See color insert following page 112) Two-dimensional input functions. (a) Input function measured in the lac promoter of E.
An Introduction to Systems Biology: Design Principles of Biological Circuits by Uri Alon