DISTILLER a data integration framework to reveal condition dependency of complex regulons in Escherichia coli.docVIP

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DISTILLER a data integration framework to reveal condition dependency of complex regulons in Escherichia coli.doc

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Open Access M d 2009LemmensetVoal.lumeetho10, Issue 3, Article R27 DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli Karen Lemmens*, Tijl De Bie??, Thomas Dhollander*, Sigrid C De Keersmaecker§, Inge M Thijs§, Geert Schoofs§, Ami De Weerdt§, Bart De Moor*, Jos Vanderleyden§, Julio Collado-Vides?, Kristof Engelen§ and Kathleen Marchal§ Addresses: *Department of Electrical engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium. ?Department of Engineering Mathematics, University of Bristol, Bristol BS8 1TR, UK. ?OKP Research Group, Katholieke Universiteit Leuven, Leuven 3000, Belgium. §Department of Microbial and Molecular systems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium. ?Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca AP 565-A, México. Correspondence: Kathleen Marchal. Email: kathleen.marchal@biw.kuleuven.be Published: 6 March 2009 Received: 16 October 2008 Revised: 15 January 2009 Accepted: 6 March 2009 Genome Biology 2009, 10:R27 (doi:10.1186/gb-2009-10-3-r27) The electronic version of this article is the complete one and can be found online at /2009/10/3/R27 ? 2009 Lemmens 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. DistillerpDISTILLER,the condition depaendatadencintegrationy and moduframeworkl rity in Esforchetherichinferenceia coli n tofwotranscriptionalks./p module networks, is presented and used to investigate Abstract We present DISTILLER, a data integration framework for the inference of transcriptional module networks. Experimental validation of predicted targets for the well-studied fumarate nitrate reductas