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Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.
PLoS Comput. Biol. 6, 31:e1000836 (2010)
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.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Genomic analysis; Expression data; Profiles; Motifs
ISSN (print) / ISBN
1553-734X
e-ISSN
1553-7358
Journal
PLoS Computational Biology
Quellenangaben
Volume: 6,
Issue: 7,
Pages: 31,
Article Number: e1000836
Publisher
Public Library of Science (PLoS)
Non-patent literature
Publications
Reviewing status
Peer reviewed