Discovery of protein-DNA interactions by penalized multivariate regression.
Discovering which regulatory proteins, especially transcription factors (TFs), are active under certain experimental conditions and identifying the corresponding binding motifs is essential for understanding the regulatory circuits that control cellular programs. The experimental methods used for this purpose are laborious. Computational methods have been proven extremely effective in identifying TF-binding motifs (TFBMs). In this article, we propose a novel computational method called MotifExpress for discovering active TFBMs. Unlike existing methods, which either use only DNA sequence information or integrate sequence information with a single-sample measurement of gene expression, MotifExpress integrates DNA sequence information with gene expression measured in multiple samples. By selecting TFBMs that are significantly associated with gene expression, we can identify active TFBMs under specific experimental conditions and thus provide clues for the construction of regulatory networks. Compared with existing methods, MotifExpress substantially reduces the number of spurious results. Statistically, MotifExpress uses a penalized multivariate regression approach with a composite absolute penalty, which is highly stable and can effectively find the globally optimal set of active motifs. We demonstrate the excellent performance of MotifExpress by applying it to synthetic data and real examples of Saccharomyces cerevisiae. MotifExpress is available at http://www.stat.illinois.edu/~pingma/MotifExpress.htm.
Zamdborg
Leonid
L
Department of Statistics, University of Illinois at Urbana-Champaign, Center for Biophysics and Computational Biology, Institute for Genomic Biology, IL, USA.
Ma
Ping
P
D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D018869:Heat-Shock Response; D015999:Multivariate Analysis; D011401:Promoter Regions, Genetic; D017346:Protein Serine-Threonine Kinases / Q000378:metabolism; D012044:Regression Analysis; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism*
D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; C512912:GCN2 protein, S cerevisiae; D017346:Protein Serine-Threonine Kinases