By Uri Alon
Provides layout ideas that govern the constitution and behaviour of organic networks equivalent to gene circuits, highlighting easy, habitual circuit components that make up the community. This booklet offers a quantitative idea for which circuits are present in a given setting and a mathematical framework for realizing organic circuits.
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Additional resources for An Introduction to Systems Biology: Design Principles of Biological Circuits
To form a self-edge, an edge needs to choose its node of origin as its destination, out of the N possible target nodes. 3) with a standard deviation that is approximately the square root of the mean (again, similar to a coin-tossing experiment with a small probability pself for heads, which approximates a Poisson process): σrand ~ E / N. 4) In the E. 1, the numbers of nodes and edges are N = 424 and E = 519. 5) In contrast, the real network has 40 self-edges, which exceeds the random networks by many standard deviations.
Thus, self-edges, and in particular negatively autoregulated genes, are a network motif. A network motif is a recurring pattern in the network that occurs far more often than at random. The next question is: Why is negative autoregulation a network motif? Does it have a useful function? 2). Our criterion for comparison will be the response time of the system. 7) For stable proteins that are not appreciably degraded in the cell, the response time is equal to the cell generation time. We will now see how the negative autoregulation network motif can help speed up transcription responses.
5 Multi-D imensional Input Functions Govern Genes with Several Inputs We just saw how Hill functions and logic functions can describe input from a single transcription factor. Many genes, however, are regulated by multiple transcription factors. In other words, many nodes in the network have two or more incoming edges. , 2003). Appendix B describes how input functions can be modeled by equilibrium binding of multiple transcription factors to the promoter. Often, multi-dimensional input functions can be usefully approximated by logic functions, just as in the case of single-input functions.
An Introduction to Systems Biology: Design Principles of Biological Circuits by Uri Alon