Gene-regulation functions (GRF) provide a unique characteristic of a 
cis-regulatory module (CRM), relating the concentrations of transcription 
factors (input) to the promoter activities (output). The challenge is to predict 
GRFs from the sequence. Here we systematically consider the lysogeny-lysis CRMs 
of different temperate bacteriophages such as the Lactobacillus casei phage A2, 
Escherichia coli phages lambda, and 186 and Lactococcal phage TP901-1. This 
study allowed explaining a recent experimental puzzle on the role of Cro protein 
in the lambda switch. Several general conclusions have been drawn: 1), 
long-range interactions, multilayer assembly and DNA looping may lead to complex 
GRFs that cannot be described by linear functions of binding site occupancies; 
2), in general, GRFs cannot be described by the Boolean logic, whereas a 
three-state non-Boolean logic suffices for the studied examples; 3), studied 
CRMs of the intact phages seemed to have a similar GRF topology (the number of 
plateaus and peaks corresponding to different expression regimes); we 
hypothesize that functionally equivalent CRMs might have topologically 
equivalent GRFs for a larger class of genetic systems; and 4) within a given GRF 
class, a set of mechanistic-to-mathematical transformations has been identified, 
which allows shaping the GRF before carrying out a system-level analysis.