期刊
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷 102, 期 20, 页码 7079-7084出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0408743102
关键词
evolutionary Monte Carlo; gene regulation; hidden Markov models; transcription factor binding sites
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.
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