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Nucleic Acids Research Advance Access published online on October 18, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm828
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© 2007 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.

Database Issue

TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors

Barrett C. Foat1, Ronald G. Tepper1,2 and Harmen J. Bussemaker1,3,*

1Department of Biological Sciences, Columbia University, New York, New York 10027, 2Integrated Program in Cellular, Molecular and Biophysical Studies and 3Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA

*To whom correspondence should be addressed. Tel: +1 212 854 9932; Fax: +1 212 865 8246; Email: hjb2004{at}columbia.edu

Received August 14, 2007. Revised September 18, 2007. Accepted September 20, 2007.

Accurate and comprehensive information about the nucleotide sequence specificity of trans-acting factors (TFs) is essential for computational and experimental analyses of gene regulatory networks. We present the Yeast Transfactome Database, a repository of sequence specificity models and condition-specific regulatory activities for a large number of DNA- and RNA-binding proteins in Saccharomyces cerevisiae. The sequence specificities in TransfactomeDB, represented as position-specific affinity matrices (PSAMs), are directly estimated from genomewide measurements of TF-binding using our previously published MatrixREDUCE algorithm, which is based on a biophysical model. For each mRNA expression profile in the NCBI Gene Expression Omnibus, we used sequence-based regression analysis to estimate the post-translational regulatory activity of each TF for which a PSAM is available. The trans-factor activity profiles across multiple experiments available in TransfactomeDB allow the user to explore potential regulatory roles of hundreds of TFs in any of thousands of microarray experiments. Our resource is freely available at http://bussemakerlab.org/TransfactomeDB/

Present address: Barrett C. Foat, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA


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