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Democratizing systems immunology with modular transcriptional repertoire analyses

Nature Reviews Immunology volume 14, pages 271–280 (2014)Cite this article

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Abstract

Individual elements that constitute the immune system have been characterized over the few past decades, mostly through reductionist approaches. The introduction of large-scale profiling platforms has more recently facilitated the assessment of these elements on a global scale. However, the analysis and the interpretation of such large-scale datasets remains a challenge and a barrier for the wider adoption of systems approaches in immunological and clinical studies. In this Innovation article, we describe an analytical strategy that relies on the a priori determination of co-dependent gene sets for a given biological system. Such modular transcriptional repertoires can in turn be used to simplify the analysis and the interpretation of large-scale datasets, and to design targeted immune fingerprinting assays and web applications that will further facilitate the dissemination of systems approaches in immunology.

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Figure 1: Modular repertoire identification.
Figure 2: Mapping perturbations of the modular repertoire.
Figure 3: Mapping perturbations of the modular repertoire across individual samples.
Figure 4: Mapping perturbations of the modular repertoire across studies.
Figure 5: Transcriptome fingerprinting assays.

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Acknowledgements

The authors would like to thank S. Presnell, M. C. Altman and E. Whalen for input and comments, B. Norris for editorial help, and C. Quinn, S. Presnell, K. Domico, E. Whalen, A. Bjork and B. Zeitner for the development of web tools. N.B. and D.C. are supported by US National Institutes of Health grants U01AI082110, U19-AI089987, U19-AI08998 and U19-AI057234. The authors apologize to those in the field whose important work was not cited here because of space limitations.

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Authors and Affiliations

  1. Damien Chaussabel is at the Benaroya Research Institute Systems Immunology Division, 1201 Ninth Street, Seattle, Washington, 98101-2795, USA.,

    Damien Chaussabel

  2. Nicole Baldwin is at the Baylor Institute for Immunology Research, Baylor Research Institute, 3434 Live Oak St, Dallas, Texas, 75204, USA.,

    Nicole Baldwin

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Correspondence to Damien Chaussabel.

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The authors are listed as inventors on patent applications and they receive funding from grants to support their research from the National Institute of Allergy and Infectious Diseases, National Institute of Health, USA.

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Online Supplementary Material: Interactive web applications for exploration of modular repertoire analysis results (PDF 85 kb)

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Chaussabel, D., Baldwin, N. Democratizing systems immunology with modular transcriptional repertoire analyses. Nat Rev Immunol 14, 271–280 (2014). https://doi.org/10.1038/nri3642

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