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Systems Genetics pp 153–188Cite as

A Suite of Tools for Biologists That Improve Accessibility and Visualization of Large Systems Genetics Datasets: Applications to the Hybrid Mouse Diversity Panel

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1488))

Abstract

In this chapter we address the recent explosion in large multilevel population studies such as the METSIM study in humans as well as large panels of animal models such as the Hybrid Mouse Diversity Panel or the BXD set of recombinant inbred strains. These studies have harnessed the increasing affordability of large-scale high-throughput profiling to gather massive quantities of data. These datasets, spread across different -omics levels (genome, transcriptome, etc.), different tissues (e.g. heart, plasma, bone) and different environmental factors (e.g. diet, drugs) each individually have led to a number of novel findings relevant to a variety of complex diseases and other phenotypes. The analysis of these results, however, is often limited to individuals with a comprehensive understanding of database languages such as SQL. In this chapter, we describe the development of a GUI-based database analysis suite, using the Hybrid Mouse Diversity Panel as an example to lay out a series of methods for visualization and integration of large systems genetics datasets. The database is based on the Shiny suite of tools in R, and is transferrable to other SQL-based datasets.

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Acknowledgments

The HMDP database was developed and is currently maintained through support from NIH grants HL30568, HL28481.

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Authors and Affiliations

  1. Department of Medicine/Division of Cardiology, University of California, Campus – 167917, BH-307 CHS, 10833 Le Conte Ave., Los Angeles, CA, USA

    Christoph D. Rau, Calvin Pan & Aldons J. Lusis

  2. Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA

    Mete Civelek

Authors
  1. Christoph D. Rau
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  2. Mete Civelek
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  3. Calvin Pan
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  4. Aldons J. Lusis
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Corresponding author

Correspondence to Aldons J. Lusis .

Editor information

Editors and Affiliations

  1. Department of Infection Genetics, Helmholtz Centre for Infection Research & University of Veterinary Medicine Hannover, Braunschweig, Niedersachsen, Germany

    Klaus Schughart

  2. Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA

    Robert W. Williams

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Rau, C.D., Civelek, M., Pan, C., Lusis, A.J. (2017). A Suite of Tools for Biologists That Improve Accessibility and Visualization of Large Systems Genetics Datasets: Applications to the Hybrid Mouse Diversity Panel. In: Schughart, K., Williams, R. (eds) Systems Genetics. Methods in Molecular Biology, vol 1488. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6427-7_7

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  • DOI: https://doi.org/10.1007/978-1-4939-6427-7_7

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6425-3

  • Online ISBN: 978-1-4939-6427-7

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