Schematic of the quantitative approach to linking CNV with gene expression in the case of 4 motifs. (*A*) Positive feedback. (*B*) Bistable feedback. (*C*) Toggle switch. (*D*) Repressilator. (*E*) Catalogs the process we consider in order from fast to slow processes (degradation of mRNA and proteins are not shown). Variables refer to concentrations of protein monomers (*x*), protein dimers (*y*), unoccupied and occupied promoters (*d*_{0} and *d*_{1}), and mRNA (*m*). Parameters κ_{±} are the dimerization and dedimerization rates, *k*_{±} are the binding and dissociation rates of the dimers to the promoter site, α is the basal transcription rate, β is the regulated transcription rate, σ is the translation rate, γ_{m} is the degradation rate of mRNA, γ_{p} and γ_{i} denote the degradation rate of proteins. The subscript *i* denotes the index of the promoter, monomer, or dimer in the motif. (*C*) The notation for the toggle switch is *i* = 1,2, and, to simplify the index notation we assume that 2 + 1 = 1; that is, the index wraps back to 1 once it becomes >2. The variables and parameters have the same meaning as in the other cases except that *d*_{0,i} and *d*_{i} denote free and occupied promoters of the *i*th gene. (*D*) For the repressilator system, we again employ our “wrapping” notation, this time using the rule 3 + 1 = 1, so that when the index becomes >3 it wraps back to 1. Note that in the motif schematics in the first column, transcription and translation are denoted using a single dashed line.

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