The Boolean Logic Assumption
Within the assumption of the Boolean logic, four principles guiding the operation of these cis-regulatory modules are : 1) The design of the cis-regulatory module determines the regulatory function. 2) In relation to development, these modules can generate both positive and negative outputs. 3) The output of each module is a product of the various operations performed on it. Common operations: “OR” logic gate- This design indicates that in an output will be given when either input is given . “AND” logic gate– In this design two different regulatory factors are necessary to make sure that a positive output results. “Toggle Switches”- This design occurs when the signal ligand is absent while the transcription factor is present; this transcription factor ends up acting as a dominant repressor. However, once the signal ligand is present the transcription factor’s role as repressor is eliminated and transcription can occur. Other Boolean logic operations can occur as well, such as sequence specific transcriptional repressors, which when they bind to the cis-regulatory module lead to an output of zero. Additionally, besides influence from the different logic operations, the output of a "cis"-regulatory module will also be influenced by prior events. 4) Cis-regulatory modules must interact with other regulatory elements. For the most part, even with the presence of functional overlap between cis-regulatory modules of a gene, the modules’ inputs and outputs tend to not be the same.
While the assumption of Boolean logic is important for systems biology, detailed studies show that in general the logic of gene regulation id not Boolean. This means, for example, that in the case of a sic-regulatory module regulated by two transcription factors, experimentally determined gene-regulation functions can not be described by the 16 possible Boolean functions of two variables. Non-Boolean extensions of the gene-regulatory logic have been proposed to correct for this issue.
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