Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules.docVIP

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Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules.doc

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Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules

Algorithms for Molecular Biology BioMedCentral Research Open Access Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules Valentina Boeva*1,2, Julien Clément3, Mireille Régnier2, Mikhail A Roytberg4,5 and Vsevolod J Makeev1,6 Address: 1Institute of Genetics and Selection of Industrial Microorganisms, GosNIIGenetika, 117545 Moscow, Russia, 2MIGEC, INRIA Rocquencourt, 78153 Le Chesnay, France, 3GREYC, CNRS UMR 6072, Laboratoire dinformatique, 14032 Caen, France, 4Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Puschino, Moscow Region, Russia, 5Puschino State University, Puschino, Moscow Region, Russia and 6Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia Email: Valentina Boeva* - valeyo@yandex.ru; Julien Clément - Julien.Clement@info.unicaen.fr; Mireille Régnier - Mireille.Regnier@inria.fr; Mikhail A Roytberg - mroytberg@impb.psn.ru; Vsevolod J Makeev - makeev@genetika.ru * Corresponding author Published: 10 October 2007 Received: 13 July 2007 Accepted: 10 October 2007 Algorithms for Molecular Biology 2007, 2:13 doi:10.1186/1748-7188-2-13 This article is available from: /content/2/1/13 ? 2007 Boeva et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: cis-Regulatory modules (CRMs) of eukaryotic genes often contain multiple binding sites for transcription factors. The phenomenon that binding sites form clusters in CRMs is exploited in many algorithms to locate CRMs in a genome. This gives rise to the problem of calculating the statistical significance of the event that multiple sites, recognized by different factors, would