Abstract
Background: Transcriptional regulation of cellular functions is carried out through a complex network of interactions among transcription factors and the promoter regions of genes and operons regulated by them.To better understand the system-level function of such networks simplification of their architecture was previously achieved by identifying the motifs present in the network, which are small, overrepresented, topologically distinct regulatory interaction patterns (subgraphs). However, the interaction of such motifs with each other, and their form of integration into the full network has not been previously examined. Results: By studying the transcriptional regulatory network of the bacterium, Escherichia coli, we demonstrate that the two previously identified motif types in the network (i.e., feed-forward loops and bi-fan motifs) do not exist in isolation, but rather aggregate into homologous motif clusters that largely overlap with known biological functions. Moreover, these clusters further coalesce into a supercluster, thus establishing distinct topological hierarchies that show global statistical properties similar to the whole network. Targeted removal of motif links disintegrates the network into small, isolated clusters, while random disruptions of equal number of links do not cause such an effect. Conclusion: Individual motifs aggregate into homologous motif clusters and a supercluster forming the backbone of the E. coli transcriptional regulatory network and play a central role in defining its global topological organization.
Keywords
transcriptional regulatory network, E coli, topological motifs, cellular functions, subgraphs
Subject Categories
Escherichia coli
Disciplines
Physics
Publisher
BioMed Central Ltd.
Publication Date
1-2004
Rights Information
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.
Rights Holder
© Dobrin et al.
Permanent URL
Recommended Citation
Dobrin, Radu; Beg, Qasim K.; Barabási, Albert-László; and Oltvai, Zoltán N., "Aggregation of topological motifs in the Escherichia coli transcriptional regulatory networks" (2004). Physics Faculty Publications. Paper 103. http://hdl.handle.net/2047/d20000676
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Notes
Originally published in BMC Bioinformatics 2004, 5:10. doi:10.1186/1471-2105-5-10