MOTIVATION: A key aspect of transcriptional regulation is the binding of transcription factors to sequence-specific binding sites that allow them to modulate the expression of nearby genes. Given models of such binding sites, one can scan regulatory regions for putative binding sites and construct a genome-wide regulatory network. In such genome-wide scans, it is crucial to control the amount of false positive predictions. Recently, several works demonstrated the benefits of modeling dependencies between positions within the binding site. Yet, computing the statistical significance of putative binding sites in this scenario remains a challenge. RESULTS: We present a general, accurate and efficient method for computing p-values of putative binding sites that is applicable to a large class of probabilistic binding site and background models. We demonstrate the accuracy of the method on synthetic and real-life data. AVAILABILITY: The procedure for scanning DNA sequences and computing the statistical significance of putative binding site scores is available upon request at http://compbio.cs.huji.ac.il/CIS/ CONTACT: nir@cs.huji.ac.il.
MOTIVATION: A key aspect of transcriptional regulation is the binding of transcription factors to sequence-specific binding sites that allow them to modulate the expression of nearby genes. Given models of such binding sites, one can scan regulatory regions for putative binding sites and construct a genome-wide regulatory network. In such genome-wide scans, it is crucial to control the amount of false positive predictions. Recently, several works demonstrated the benefits of modeling dependencies between positions within the binding site. Yet, computing the statistical significance of putative binding sites in this scenario remains a challenge. RESULTS: We present a general, accurate and efficient method for computing p-values of putative binding sites that is applicable to a large class of probabilistic binding site and background models. We demonstrate the accuracy of the method on synthetic and real-life data. AVAILABILITY: The procedure for scanning DNA sequences and computing the statistical significance of putative binding site scores is available upon request at http://compbio.cs.huji.ac.il/CIS/ CONTACT: nir@cs.huji.ac.il.
Authors: Ilan Wapinski; Jenna Pfiffner; Courtney French; Amanda Socha; Dawn Anne Thompson; Aviv Regev Journal: Proc Natl Acad Sci U S A Date: 2010-03-08 Impact factor: 11.205
Authors: Ruth Perets; Tommy Kaplan; Ilan Stein; Guy Hidas; Shay Tayeb; Eti Avraham; Yinon Ben-Neriah; Itamar Simon; Eli Pikarsky Journal: PLoS One Date: 2012-10-04 Impact factor: 3.240
Authors: Tommy Kaplan; Xiao-Yong Li; Peter J Sabo; Sean Thomas; John A Stamatoyannopoulos; Mark D Biggin; Michael B Eisen Journal: PLoS Genet Date: 2011-02-03 Impact factor: 5.917