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

doi:10.1186/gb-2009-10-3-r27

Genome Biology

Volume 10
Issue 3

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Lemmens K
De Bie T
Dhollander T
De Keersmaecker SC
Thijs IM
Schoofs G
De Weerdt A
De Moor B
Vanderleyden J
Collado-Vides J
Engelen K
Marchal K

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Lemmens K
De Bie T
Dhollander T
De Keersmaecker SC
Thijs IM
Schoofs G
De Weerdt A
De Moor B
Vanderleyden J
Collado-Vides J
Engelen K
Marchal K
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DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

Karen Lemmens¹ , Tijl De Bie²^,3 , Thomas Dhollander¹ , Sigrid C De Keersmaecker⁴ , Inge M Thijs⁴ , Geert Schoofs⁴ , Ami De Weerdt⁴ , Bart De Moor¹ , Jos Vanderleyden⁴ , Julio Collado-Vides⁵ , Kristof Engelen⁴ and Kathleen Marchal⁴

¹Department of Electrical engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium

²Department of Engineering Mathematics, University of Bristol, Bristol BS8 1TR, UK

³OKP Research Group, Katholieke Universiteit Leuven, Leuven 3000, Belgium

⁴Department of Microbial and Molecular systems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium

⁵Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca AP 565-A, México

author email corresponding author email

Genome Biology 2009, 10:R27doi:10.1186/gb-2009-10-3-r27


Published:	6 March 2009

Subject areas: Bioinformatics, Genome studies, Molecular biology

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 reductase regulator showed the effectiveness of our approach in Escherichia coli. In addition, the condition dependency and modularity of the inferred transcriptional network was studied. Surprisingly, the level of regulatory complexity seemed lower than that which would be expected from RegulonDB, indicating that complex regulatory programs tend to decrease the degree of modularity.