By Uri Alon
Offers layout ideas that govern the constitution and behaviour of organic networks corresponding to gene circuits, highlighting uncomplicated, habitual circuit components that make up the community. This e-book presents a quantitative concept for which circuits are present in a given surroundings and a mathematical framework for realizing organic circuits.
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Extra info for An Introduction to Systems Biology: Design Principles of Biological Circuits
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. For example, consider genes regulated by two activators. Many genes require binding of both activator proteins to the promoter in order to show significant expression. 6) For other genes, binding of either activator is sufficient. 7) Not all genes have Boolean-like input functions.
Edges denoted X → Y mean that gene X encodes for a transcription factor protein that binds the promoter of gene Y and modulates its rate of transcription. Thus, the protein encoded by gene X changes the rate of production of the protein encoded by gene Y. Protein Y, in turn, might be a transcription factor that changes the rate of production of Z, and so on, forming an interaction network. Most nodes in the network stand for genes that encode proteins that are not transcription factors. These proteins carry out the various functions of the cell.
3. Time-dependent production and decay. A gene Y with simple regulation has a timedependent production rate b(t) and a time-dependent degradation rate α(t). Solve for its concentration as a function of time. 4. Cascades. Consider a cascade of three activators, X → Y → Z. Protein X is initially present in the cell in its inactive from. The input signal of X, Sx, appears at time t = 0. As a result, X rapidly becomes active and binds the promoter of gene Y, so that protein Y starts to be produced at rate b.
An Introduction to Systems Biology: Design Principles of Biological Circuits by Uri Alon