FIGURE 1 

(A) Schematic diagram of a hypothetical bacterial operon, represented by a single gene Y, which is regulated by a protein X₁ and a protein complex X₂X₃. (B) Within its dynamic range, the level of the transcript y may be modeled as a function of transcripts of the regulatory proteins X₁, X_2, and X₃. The min function captures the notion of cooperativity, and the general form of g incorporates saturation effects. On the genome scale, the initial model for regulation of y would involve all possible transcription factors, and would greatly benefit from parameter shrinkage by LASSO. (C) This table illustrates the representative power of the chosen design matrix. The model can capture AND, OR, and XOR logical functions and saturation effects (not shown). Assigning the shown values to the coefficients from (B) would cause the model to represent the corresponding logical function for the interaction of X₂ and X₃.