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. 2009 May;5(5):e1000385.
doi: 10.1371/journal.pcbi.1000385. Epub 2009 May 29.

Hypergraphs and cellular networks

Steffen Klamt  1 , Utz-Uwe Haus, Fabian Theis
Affiliations

Hypergraphs and cellular networks

Steffen Klamt et al. PLoS Comput Biol. 2009 May.
No abstract available

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Examples of undirected (A,B) and directed (C,D) hypergraphs arising in the context of biological networks analysis.
Detailed explanations are given in the text.
Figure 2
Figure 2. Generating a hypergraph null model by rewiring.
Choose two distinct hyperedges and two different vertices contained in either of the two. Then swap them. Clearly this operation keeps both degree distributions fixed. After a certain number of iterations, the thus-generated Markov chain produces independent samples of the underlying random hypergraph with given degree distributions. In the figure, this is illustrated using the in-this-case simpler-to-visualize bipartite version. The gray double-arrows indicate edges to be swapped. Each of the three swaps, (A,H2)–(C,H3), (B,H1)–(E,H3), and (B,H3)–(D,H1), does not change the vertex and edge degrees. Significance analysis of the CORUM protein complex hypergraph was done in using this idea.
See this image and copyright information in PMC

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References

    1. Aittokallio T, Schwikowski V. Graph-based methods for analysing networks in cell biology. Brief Bioinform. 2006;7:243–255. - PubMed
    1. Gavin AC, Bösche M, Krause R, Grandi P, Marzioch M, et al. Functional organization of the yeast proteome by systematic analysis of the protein complexes. Nature. 2002;415:141–147. - PubMed
    1. Gagneur J, Krause R, Bouwmeester T, Casari G. Modular decomposition of protein-protein interaction networks. Genome Biol. 2004;5:R57. - PMC - PubMed
    1. Wuchty S, Almaas E. Peeling the yeast proteome network. Proteomics. 2005;5:444–449. - PubMed
    1. Ramadan E, Tarafdar A, Pothen A. A hypergraph model for the yeast protein complex network. In: Proceedings of the Sixth IEEE Workshop on High Performance Computational Biology; April 26, 2004; Santa Fe, New Mexico, United States 2004

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