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Bioinformatics Advance Access published online on September 6, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn467
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

STREAM: Static Thermodynamic REgulAtory Model of transcription

Denis C. Bauer 1 and Timothy L. Bailey 1,*

1Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld. 4072 Australia

*To whom correspondence should be addressed. Timothy L. Bailey, E-mail: t.bailey{at}imb.uq.edu.au


  Abstract

Motivation: Understanding the transcriptional regulation of a gene in detail is a crucial step towards uncovering and ultimately utilizing the regulatory grammar of the genome. Modeling transcriptional regulation using thermodynamic equations has become an increasingly important approach towards this goal.

Here, we present STREAM, the first publicly available framework for modeling, visualizing, and predicting the regulation of the transcription rate of a target gene. Given the concentrations of a set of transcription factors, the transcription factor binding sites in a regulatory DNA region, and the transcription rate of the target gene, STREAM will optimize its parameters to generate a model that best fits the input data. This trained model can then be used to (a) validate that the given set of TFs is able to regulate the target gene and (b) to predict the transcription rate under different conditions (e.g. different tissues, knockout/additional TFs or mutated/missing TFBS).

Availability: The platform independent executable of STREAM, as well as a tutorial and the full documentation, are available at http://bioinformatics.org.au/stream/. STREAM requires Java version 5 or higher.

Contact: d.bauer{at}imb.uq.edu.au, t.bailey{at}imb.uq.edu.au

Associate Editor: Dr. Joaquin Dopazo

Received on June 27, 2008; revised on August 11, 2008; accepted on August 28, 2008

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D. C. Bauer and T. L. Bailey
Optimizing static thermodynamic models of transcriptional regulation
Bioinformatics, July 1, 2009; 25(13): 1640 - 1646.
[Abstract] [Full Text] [PDF]


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