Reverse-engineering transcription control networks

Timothy S Gardner; Jeremiah J Faith

doi:10.1016/j.plrev.2005.01.001

Reverse-engineering transcription control networks

Phys Life Rev. 2005 Mar;2(1):65-88. doi: 10.1016/j.plrev.2005.01.001.

Authors

Timothy S Gardner¹, Jeremiah J Faith

Affiliation

¹ Department of Biomedical Engineering, Boston University, 44 Cummington St., Boston, MA 02215, USA.

PMID: 20416858
DOI: 10.1016/j.plrev.2005.01.001

Abstract

Microarray technologies, which enable the simultaneous measurement of all RNA transcripts in a cell, have spawned the development of algorithms for reverse-engineering transcription control networks. In this article, we classify the algorithms into two general strategies: physical modeling and influence modeling. We discuss the biological and computational principles underlying each strategy, and provide leading examples of each. We also discuss the practical considerations for developing and applying the various methods.