Implementing arithmetic and other analytic operations by transcriptional regulation.

@article{citeulike:2730536, abstract = {The transcriptional regulatory machinery of a gene can be viewed as a computational device, with transcription factor concentrations as inputs and expression level as the output. This view begs the question: what kinds of computations are possible? We show that different parameterizations of a simple chemical kinetic model of transcriptional regulation are able to approximate all four standard arithmetic operations: addition, subtraction, multiplication, and division, as well as various equality and inequality operations. This contrasts with other studies that emphasize logical or digital notions of computation in biological networks. We analyze the accuracy and precision of these approximations, showing that they depend on different sets of parameters, and are thus independently tunable. We demonstrate that networks of these "arithmetic" genes can be combined to accomplish yet more complicated computations by designing and simulating a network that detects statistically significant elevations in a time-varying signal. We also consider the much more general problem of approximating analytic functions, showing that this can be achieved by allowing multiple transcription factor binding sites on the promoter. These observations are important for the interpretation of naturally occurring networks and imply new possibilities for the design of synthetic networks.}, address = {Department of Human Genetics, McGill University, Montreal, Quebec, Canada.}, author = {Cory, S. M. and Perkins, T. J. }, citeulike-article-id = {2730536}, doi = {10.1371/journal.pcbi.1000064}, issn = {1553-7358}, journal = {PLoS computational biology}, keywords = {computational\_biology, synthetic\_biology}, month = {April}, number = {4}, posted-at = {2008-06-04 18:45:50}, priority = {4}, title = {Implementing arithmetic and other analytic operations by transcriptional regulation.}, url = {http://dx.doi.org/10.1371/journal.pcbi.1000064}, volume = {4}, year = {2008} }

TY - JOUR ID - citeulike:2730536 L3 - citeulike-article-id:2730536 TI - Implementing arithmetic and other analytic operations by transcriptional regulation. JF - PLoS computational biology VL - 4 IS - 4 AD - Department of Human Genetics, McGill University, Montreal, Quebec, Canada. SN - 1553-7358 N2 - The transcriptional regulatory machinery of a gene can be viewed as a computational device, with transcription factor concentrations as inputs and expression level as the output. This view begs the question: what kinds of computations are possible? We show that different parameterizations of a simple chemical kinetic model of transcriptional regulation are able to approximate all four standard arithmetic operations: addition, subtraction, multiplication, and division, as well as various equality and inequality operations. This contrasts with other studies that emphasize logical or digital notions of computation in biological networks. We analyze the accuracy and precision of these approximations, showing that they depend on different sets of parameters, and are thus independently tunable. We demonstrate that networks of these "arithmetic" genes can be combined to accomplish yet more complicated computations by designing and simulating a network that detects statistically significant elevations in a time-varying signal. We also consider the much more general problem of approximating analytic functions, showing that this can be achieved by allowing multiple transcription factor binding sites on the promoter. These observations are important for the interpretation of naturally occurring networks and imply new possibilities for the design of synthetic networks. KW - computational_biology KW - synthetic_biology AU - Cory, SM AU - Perkins, TJ PY - 2008/04// UR - http://dx.doi.org/10.1371/journal.pcbi.1000064 ER -