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Regulatory Motif Finding By Logic Regression, Sunduz Keles, Mark J. Van Der Laan, Chris Vulpe
Regulatory Motif Finding By Logic Regression, Sunduz Keles, Mark J. Van Der Laan, Chris Vulpe
U.C. Berkeley Division of Biostatistics Working Paper Series
Multiple transcription factors coordinately control transcriptional regulation of genes in eukaryotes. Although multiple computational methods consider the identification of individual transcription factor binding sites (TFBSs), very few focus on the interactions between these sites. We consider finding transcription factor binding sites and their context specific interactions using microarray gene expression data. We devise a hybrid approach called LogicMotif composed of a TFBS identification method combined with the new regression methodology logic regression of Ruczinski et al. (2003). LogicMotif has two steps: First potential binding sites are identified from transcription control regions of genes of interest. Various available methods can be …
A Statistical Method For Constructing Transcriptional Regulatory Networks Using Gene Expression And Sequence Data , Biao Xing, Mark J. Van Der Laan
A Statistical Method For Constructing Transcriptional Regulatory Networks Using Gene Expression And Sequence Data , Biao Xing, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
Transcriptional regulation is one of the most important means of gene regulation. Uncovering transcriptional regulatory network helps us to understand the complex cellular process. In this paper, we describe a comprehensive statistical approach for constructing the transcriptional regulatory network using data of gene expression, promoter sequence, and transcription factor binding sites. Our simulation studies show that the overall and false positive error rates in the estimated transcriptional regulatory network are expected to be small if the systematic noise in the constructed feature matrix is small. Our analysis based on 658 microarray experiments on yeast gene expression programs and 46 transcription …