Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.

The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data, one can identify functional properties of the TRN and gain general insight into transcrip...

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Autores principales:	Carsten Marr, Fabian J Theis, Larry S Liebovitch, Marc-Thorsten Hütt
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/0717fc5430b74ee9a4642778de2a7b4e
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spelling	oai:doaj.org-article:0717fc5430b74ee9a4642778de2a7b4e2021-12-02T19:58:19ZPatterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.1553-734X1553-735810.1371/journal.pcbi.1000836https://doaj.org/article/0717fc5430b74ee9a4642778de2a7b4e2010-07-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20617198/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data, one can identify functional properties of the TRN and gain general insight into transcriptional control. We define the subnet of a node as the subgraph consisting of all nodes topologically downstream of the node, including itself. Using a large set of microarray expression data of the bacterium Escherichia coli, we find that the gene expression in different subnets exhibits a structured pattern in response to environmental changes and genotypic mutation. Subnets with fewer changes in their expression pattern have a higher fraction of feed-forward loop motifs and a lower fraction of small RNA targets within them. Our study implies that the TRN consists of several scales of regulatory organization: (1) subnets with more varying gene expression controlled by both transcription factors and post-transcriptional RNA regulation and (2) subnets with less varying gene expression having more feed-forward loops and less post-transcriptional RNA regulation.Carsten MarrFabian J TheisLarry S LiebovitchMarc-Thorsten HüttPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 6, p e1000836 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Carsten Marr Fabian J Theis Larry S Liebovitch Marc-Thorsten Hütt Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.
description	The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data, one can identify functional properties of the TRN and gain general insight into transcriptional control. We define the subnet of a node as the subgraph consisting of all nodes topologically downstream of the node, including itself. Using a large set of microarray expression data of the bacterium Escherichia coli, we find that the gene expression in different subnets exhibits a structured pattern in response to environmental changes and genotypic mutation. Subnets with fewer changes in their expression pattern have a higher fraction of feed-forward loop motifs and a lower fraction of small RNA targets within them. Our study implies that the TRN consists of several scales of regulatory organization: (1) subnets with more varying gene expression controlled by both transcription factors and post-transcriptional RNA regulation and (2) subnets with less varying gene expression having more feed-forward loops and less post-transcriptional RNA regulation.
format	article
author	Carsten Marr Fabian J Theis Larry S Liebovitch Marc-Thorsten Hütt
author_facet	Carsten Marr Fabian J Theis Larry S Liebovitch Marc-Thorsten Hütt
author_sort	Carsten Marr
title	Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.
title_short	Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.
title_full	Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.
title_fullStr	Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.
title_full_unstemmed	Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.
title_sort	patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of escherichia coli.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/0717fc5430b74ee9a4642778de2a7b4e
work_keys_str_mv	AT carstenmarr patternsofsubnetusagerevealdistinctscalesofregulationinthetranscriptionalregulatorynetworkofescherichiacoli AT fabianjtheis patternsofsubnetusagerevealdistinctscalesofregulationinthetranscriptionalregulatorynetworkofescherichiacoli AT larrysliebovitch patternsofsubnetusagerevealdistinctscalesofregulationinthetranscriptionalregulatorynetworkofescherichiacoli AT marcthorstenhutt patternsofsubnetusagerevealdistinctscalesofregulationinthetranscriptionalregulatorynetworkofescherichiacoli
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Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.

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