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

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 dep...

Descripción completa

Detalles Bibliográficos
Autores principales: Lemmens, Karen, De Bie, Tijl, Dhollander, Thomas, De Keersmaecker, Sigrid C, Thijs, Inge M, Schoofs, Geert, De Weerdt, Ami, De Moor, Bart, Vanderleyden, Jos, Collado-Vides, Julio, Engelen, Kristof, Marchal, Kathleen
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690998/
https://www.ncbi.nlm.nih.gov/pubmed/19265557
http://dx.doi.org/10.1186/gb-2009-10-3-r27
_version_ 1782167864165269504
author Lemmens, Karen
De Bie, Tijl
Dhollander, Thomas
De Keersmaecker, Sigrid C
Thijs, Inge M
Schoofs, Geert
De Weerdt, Ami
De Moor, Bart
Vanderleyden, Jos
Collado-Vides, Julio
Engelen, Kristof
Marchal, Kathleen
author_facet Lemmens, Karen
De Bie, Tijl
Dhollander, Thomas
De Keersmaecker, Sigrid C
Thijs, Inge M
Schoofs, Geert
De Weerdt, Ami
De Moor, Bart
Vanderleyden, Jos
Collado-Vides, Julio
Engelen, Kristof
Marchal, Kathleen
author_sort Lemmens, Karen
collection PubMed
description 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.
format Text
id pubmed-2690998
institution National Center for Biotechnology Information
language English
publishDate 2009
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-26909982009-06-04 DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli Lemmens, Karen De Bie, Tijl Dhollander, Thomas De Keersmaecker, Sigrid C Thijs, Inge M Schoofs, Geert De Weerdt, Ami De Moor, Bart Vanderleyden, Jos Collado-Vides, Julio Engelen, Kristof Marchal, Kathleen Genome Biol Method 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. BioMed Central 2009 2009-03-06 /pmc/articles/PMC2690998/ /pubmed/19265557 http://dx.doi.org/10.1186/gb-2009-10-3-r27 Text en Copyright © 2009 Lemmens et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Lemmens, Karen
De Bie, Tijl
Dhollander, Thomas
De Keersmaecker, Sigrid C
Thijs, Inge M
Schoofs, Geert
De Weerdt, Ami
De Moor, Bart
Vanderleyden, Jos
Collado-Vides, Julio
Engelen, Kristof
Marchal, Kathleen
DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli
title DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli
title_full DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli
title_fullStr DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli
title_full_unstemmed DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli
title_short DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli
title_sort distiller: a data integration framework to reveal condition dependency of complex regulons in escherichia coli
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690998/
https://www.ncbi.nlm.nih.gov/pubmed/19265557
http://dx.doi.org/10.1186/gb-2009-10-3-r27
work_keys_str_mv AT lemmenskaren distilleradataintegrationframeworktorevealconditiondependencyofcomplexregulonsinescherichiacoli
AT debietijl distilleradataintegrationframeworktorevealconditiondependencyofcomplexregulonsinescherichiacoli
AT dhollanderthomas distilleradataintegrationframeworktorevealconditiondependencyofcomplexregulonsinescherichiacoli
AT dekeersmaeckersigridc distilleradataintegrationframeworktorevealconditiondependencyofcomplexregulonsinescherichiacoli
AT thijsingem distilleradataintegrationframeworktorevealconditiondependencyofcomplexregulonsinescherichiacoli
AT schoofsgeert distilleradataintegrationframeworktorevealconditiondependencyofcomplexregulonsinescherichiacoli
AT deweerdtami distilleradataintegrationframeworktorevealconditiondependencyofcomplexregulonsinescherichiacoli
AT demoorbart distilleradataintegrationframeworktorevealconditiondependencyofcomplexregulonsinescherichiacoli
AT vanderleydenjos distilleradataintegrationframeworktorevealconditiondependencyofcomplexregulonsinescherichiacoli
AT colladovidesjulio distilleradataintegrationframeworktorevealconditiondependencyofcomplexregulonsinescherichiacoli
AT engelenkristof distilleradataintegrationframeworktorevealconditiondependencyofcomplexregulonsinescherichiacoli
AT marchalkathleen distilleradataintegrationframeworktorevealconditiondependencyofcomplexregulonsinescherichiacoli

Ejemplares similares