Abstract
There are many instances where the circuit topology of the GRN is known, but the logic function of each node in this topology is not. In addition, a number N of measurements on the gene expression states of the GRN are given or are known. Using this information, this chapter will derive SAT based algorithms which yield the logic of every node in the GRN so that the N gene expression measurements and topology are satisfied. If N is too small, then a multitude of GRNs may satisfy the observed behavior, yielding a reduced certainty in the final result due to lack of data. We will also study the behavior of the number of satisfying GRNs with respect to the number of observations N.
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Notes
- 1.
Part of the data reported in this chapter is reprinted with permission from “Determining Gene Function in Boolean Networks using Boolean Satisfiability” by Pey-Chang Kent Lin, Sunil P. Khatri. IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) 2012, Dec. 2012, pp. 1–4, Copyright 2012 by IEEE
- 2.
The cofactor of \(S(x_1, \ldots x_i \ldots x_n)\) wrt x i is \(S_{x_i}(x_1, \ldots x_i \ldots x_n) = S(x_1, \ldots x_i=1 \ldots x_n)\)
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Lin, PC., Khatri, S. (2014). Determining Gene Function in Boolean Networks using SAT. In: Logic Synthesis for Genetic Diseases. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-9429-4_3
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DOI: https://doi.org/10.1007/978-1-4614-9429-4_3
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