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  • Protocol
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NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data

Nature Protocols volume 10, pages 823–844 (2015)Cite this article

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Abstract

Meta-analysis of gene expression data sets is increasingly performed to help identify robust molecular signatures and to gain insights into underlying biological processes. The complicated nature of such analyses requires both advanced statistics and innovative visualization strategies to support efficient data comparison, interpretation and hypothesis generation. NetworkAnalyst (http://www.networkanalyst.ca) is a comprehensive web-based tool designed to allow bench researchers to perform various common and complex meta-analyses of gene expression data via an intuitive web interface. By coupling well-established statistical procedures with state-of-the-art data visualization techniques, NetworkAnalyst allows researchers to easily navigate large complex gene expression data sets to determine important features, patterns, functions and connections, thus leading to the generation of new biological hypotheses. This protocol provides a step-wise description of how to effectively use NetworkAnalyst to perform network analysis and visualization from gene lists; to perform meta-analysis on gene expression data while taking into account multiple metadata parameters; and, finally, to perform a meta-analysis of multiple gene expression data sets. NetworkAnalyst is designed to be accessible to biologists rather than to specialist bioinformaticians. The complete protocol can be executed in ∼1.5 h. Compared with other similar web-based tools, NetworkAnalyst offers a unique visual analytics experience that enables data analysis within the context of protein-protein interaction networks, heatmaps or chord diagrams. All of these analysis methods provide the user with supporting statistical and functional evidence.

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Figure 1: NetworkAnalyst analysis flowchart.
Figure 2: Navigations in NetworkAnalyst.
Figure 3: Organization of components in Network Viewer.
Figure 4: Network customization and module extraction.
Figure 5: Screenshot of the interface for differential expression analysis.
Figure 6: A chord diagram comparing six analysis results.
Figure 7: Visual analytics with heatmaps.
Figure 8: Upload and process multiple data sets for meta-analysis.

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Accession codes

Accessions

Gene Expression Omnibus

Swiss-Prot

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Acknowledgements

The authors thank the Canadian Institutes for Health Research (CIHR) for financial support.

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Authors and Affiliations

  1. Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada

    Jianguo Xia, Erin E Gill & Robert E W Hancock

  2. and Department of Animal Science, Institute of Parasitology, McGill University, Ste. Ann de Bellevue, Québec, Canada

    Jianguo Xia

  3. Department of Microbiology and Immunology, McGill University, Montreal, Québec, Canada

    Jianguo Xia

  4. Wellcome Trust Sanger Institute, Hinxton, United Kingdom

    Robert E W Hancock

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Contributions

J.X. developed NetworkAnalyst and prepared the protocol, E.E.G. tested the tool and the protocol and R.E.W.H. participated in all processes. All authors have read and approved the paper.

Corresponding authors

Correspondence to Jianguo Xia or Robert E W Hancock.

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Xia, J., Gill, E. & Hancock, R. NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data. Nat Protoc 10, 823–844 (2015). https://doi.org/10.1038/nprot.2015.052

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