De novo cis-regulatory module elicitation for eukaryotic genomes

Gupta, M. and Liu, J.S. (2005) De novo cis-regulatory module elicitation for eukaryotic genomes. Proceedings of the National Academy of Sciences of the United States of America, 102(20), pp. 7079-7084. (doi: 10.1073/pnas.0408743102)

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Abstract

Transcription regulation is controlled by coordinated binding of one or more transcription factors in the promoter regions of genes. In many species, especially higher eukaryotes, transcription factor binding sites tend to occur as homotypic or heterotypic clusters, also known as cis-regulatory modules. The number of sites and distances between the sites, however, vary greatly in a module. We propose a statistical model to describe the underlying cluster structure as well as individual motif conservation and develop a Monte Carlo motif screening strategy for predicting novel regulatory modules in upstream sequences of coregulated genes. We demonstrate the power of the method with examples ranging from bacterial to insect and human genomes.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Gupta, Professor Mayetri
Authors: Gupta, M., and Liu, J.S.
College/School:College of Science and Engineering > School of Mathematics and Statistics > Statistics
Journal Name:Proceedings of the National Academy of Sciences of the United States of America
ISSN:0027-8424
Published Online:09 May 2005

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