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NetGestalt: integrating multidimensional omics data over biological networks

Nature Methods volume 10, pages 597–598 (2013)Cite this article

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NetGestalt relies on a computational algorithm, available as the R package NetSAM (network seriation and modularization), for revealing hierarchical organization of biological networks (Supplementary Methods and Supplementary Fig. 1). Using protein-protein interaction networks from human and mouse as examples, we showed that NetSAM could identify biologically coherent modules at different scales and create functionally meaningful one-dimensional ordering of the genes (Supplementary Note 1, Supplementary Table 1 and Supplementary Fig. 2). Here we applied NetGestalt to a hierarchically and modularly organized human protein-protein interaction network based on interaction data from the Human Protein Reference Database (http://www.hprd.org/). We used two examples to demonstrate the features of NetGestalt and its potential in revealing important novel biological insights (Supplementary Note 1 and Supplementary Figs. 3–5).

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Figure 1: One-dimensional layout of a network preserves the hierarchical modular organization information.

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Acknowledgements

This work was supported by the US National Institutes of Health grants R01 GM088822, U24 CA159988 and P50 MH096972. This work was conducted in part using the resources of the Advanced Computing Center for Research and Education at Vanderbilt University.

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Author notes

  1. Zhiao Shi and Jing Wang: These authors contributed equally to this work.

Authors and Affiliations

  1. Advanced Computing Center for Research and Education, Vanderbilt University, Nashville, Tennessee, USA

    Zhiao Shi

  2. Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA

    Zhiao Shi

  3. Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, USA

    Jing Wang & Bing Zhang

  4. Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, USA

    Bing Zhang

Authors
  1. Zhiao Shi
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  2. Jing Wang
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  3. Bing Zhang
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Correspondence to Bing Zhang.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5, Supplementary Tables 1–5, Supplementary Methods and Supplementary Notes 1 and 2 (PDF 6803 kb)

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Shi, Z., Wang, J. & Zhang, B. NetGestalt: integrating multidimensional omics data over biological networks. Nat Methods 10, 597–598 (2013). https://doi.org/10.1038/nmeth.2517

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