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Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks

(2011) MOLECULAR BIOSYSTEMS. 7(10). p.2769-2778
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Topological network motifs represent functional relationships within and between regulatory and protein-protein interaction networks. Enriched motifs often aggregate into self-contained units forming functional modules. Theoretical models for network evolution by duplication-divergence mechanisms and for network topology by hierarchical scale-free networks have suggested a one-to-one relation between network motif enrichment and aggregation, but this relation has never been tested quantitatively in real biological interaction networks. Here we introduce a novel method for assessing the statistical significance of network motif aggregation and for identifying clusters of overlapping network motifs. Using an integrated network of transcriptional, posttranslational and protein-protein interactions in yeast we show that network motif aggregation reflects a local modularity property which is independent of network motif enrichment. In particular our method identified novel functional network themes for a set of motifs which are not enriched yet aggregate significantly and challenges the conventional view that network motif enrichment is the most basic organizational principle of complex networks.
Keywords
BUDDING YEAST, PHOSPHORYLATION, COMPLEX NETWORKS, YEAST SACCHAROMYCES-CEREVISIAE, DEPENDENT PROTEIN-KINASE, CYCLE-REGULATED GENES, CELL-CYCLE, ESCHERICHIA-COLI, TRANSCRIPTIONAL REGULATION, MODULARITY

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Citation

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Chicago
Michoel, Tom, Anagha Joshi, Bruno Nachtergaele, and Yves Van de Peer. 2011. “Enrichment and Aggregation of Topological Motifs Are Independent Organizational Principles of Integrated Interaction Networks.” Molecular Biosystems 7 (10): 2769–2778.
APA
Michoel, T., Joshi, A., Nachtergaele, B., & Van de Peer, Y. (2011). Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks. MOLECULAR BIOSYSTEMS, 7(10), 2769–2778.
Vancouver
1.
Michoel T, Joshi A, Nachtergaele B, Van de Peer Y. Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks. MOLECULAR BIOSYSTEMS. 2011;7(10):2769–78.
MLA
Michoel, Tom, Anagha Joshi, Bruno Nachtergaele, et al. “Enrichment and Aggregation of Topological Motifs Are Independent Organizational Principles of Integrated Interaction Networks.” MOLECULAR BIOSYSTEMS 7.10 (2011): 2769–2778. Print.
@article{1937416,
  abstract     = {Topological network motifs represent functional relationships within and between regulatory and protein-protein interaction networks. Enriched motifs often aggregate into self-contained units forming functional modules. Theoretical models for network evolution by duplication-divergence mechanisms and for network topology by hierarchical scale-free networks have suggested a one-to-one relation between network motif enrichment and aggregation, but this relation has never been tested quantitatively in real biological interaction networks. Here we introduce a novel method for assessing the statistical significance of network motif aggregation and for identifying clusters of overlapping network motifs. Using an integrated network of transcriptional, posttranslational and protein-protein interactions in yeast we show that network motif aggregation reflects a local modularity property which is independent of network motif enrichment. In particular our method identified novel functional network themes for a set of motifs which are not enriched yet aggregate significantly and challenges the conventional view that network motif enrichment is the most basic organizational principle of complex networks.},
  author       = {Michoel, Tom and Joshi, Anagha and Nachtergaele, Bruno and Van de Peer, Yves},
  issn         = {1742-206X},
  journal      = {MOLECULAR BIOSYSTEMS},
  keyword      = {BUDDING YEAST,PHOSPHORYLATION,COMPLEX NETWORKS,YEAST SACCHAROMYCES-CEREVISIAE,DEPENDENT PROTEIN-KINASE,CYCLE-REGULATED GENES,CELL-CYCLE,ESCHERICHIA-COLI,TRANSCRIPTIONAL REGULATION,MODULARITY},
  language     = {eng},
  number       = {10},
  pages        = {2769--2778},
  title        = {Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks},
  url          = {http://dx.doi.org/10.1039/c1mb05241a},
  volume       = {7},
  year         = {2011},
}

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