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Network visualization and analysis of gene expression data using BioLayout Express3D

Nature Protocols volume 4, pages 1535–1550 (2009)Cite this article

Abstract

Network analysis has an increasing role in our effort to understand the complexity of biological systems. This is because of our ability to generate large data sets, where the interaction or distance between biological components can be either measured experimentally or calculated. Here we describe the use of BioLayout Express3D, an application that has been specifically designed for the integration, visualization and analysis of large network graphs derived from biological data. We describe the basic functionality of the program and its ability to display and cluster large graphs in two- and three-dimensional space, thereby rendering graphs in a highly interactive format. Although the program supports the import and display of various data formats, we provide a detailed protocol for one of its unique capabilities, the network analysis of gene expression data and a more general guide to the manipulation of graphs generated from various other data types.

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Figure 1
Figure 2
Figure 3
Figure 4: The Class Viewer on top with the main BioLayout Express3D graph window below.
Figure 5: Rendering of GraphML files in BioLayout Express3D.
Figure 6: Rendering of pathways in BioLayout Express3D.

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Acknowledgements

We thank all those who have been involved with the development of BioLayout Express3D over the years including Leon Goldovsky, Markus Brosch, Ildefonso Cases and Christos Ouzounis. We also thank the BBSRC who are currently funding the development of the program (BB/F003722/1) together with the Wellcome Trust (GR077040RP) who previously provided support.

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Authors and Affiliations

  1. The Roslin Institute, R(D)SVS, University of Edinburgh, Roslin BioCentre, Midlothian, Scotland, UK

    Athanasios Theocharidis & Tom C Freeman

  2. EMBL—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,

    Stjin van Dongen & Anton J Enright

Authors
  1. Athanasios Theocharidis
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  2. Stjin van Dongen
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  3. Anton J Enright
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  4. Tom C Freeman
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Contributions

T.C.F., A.T., S.v.D. and A.J.E. wrote this paper. T.C.F. and A.T. conceived and designed the individual protocols.

Corresponding author

Correspondence to Tom C Freeman.

Supplementary information

Supplementary Manual

BioLayout Express3D manual providing details of all the functions within the tool. (PDF 1503 kb)

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Theocharidis, A., van Dongen, S., Enright, A. et al. Network visualization and analysis of gene expression data using BioLayout Express3D. Nat Protoc 4, 1535–1550 (2009). https://doi.org/10.1038/nprot.2009.177

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