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Science 325 (5939): 429-432

Copyright © 2009 by the American Association for the Advancement of Science

Transcriptional Regulatory Circuits: Predicting Numbers from Alphabets

Harold D. Kim,1,* Tal Shay,2,* Erin K. O’Shea,1 Aviv Regev2,{dagger}

Abstract: Transcriptional regulatory circuits govern how cis and trans factors transform signals into messenger RNA (mRNA) expression levels. With advances in quantitative and high-throughput technologies that allow measurement of gene expression state in different conditions, data that can be used to build and test models of transcriptional regulation is being generated at a rapid pace. Here, we review experimental and computational methods used to derive detailed quantitative circuit models on a small scale and cruder, genome-wide models on a large scale. We discuss the potential of combining small- and large-scale approaches to understand the working and wiring of transcriptional regulatory circuits.

1 Howard Hughes Medical Institute, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Departments of Molecular and Cellular Biology and Chemistry and Chemical Biology, Cambridge, MA 02138, USA.
2 Department of Biology, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: aregev{at}

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