title: A Suite of Tools for Biologists That Improve Accessibility and Visualization of Large Systems Genetics Datasets: Applications to the Hybrid Mouse Diversity Panel.
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.
authors.affiliation: Department of Medicine/Division of Cardiology, University of California, Campus - 167917, BH-307 CHS, 10833 Le Conte Ave., Los Angeles, CA, USA.
authors.forename: Christoph D
authors.initials: CD
authors.lastname: Rau
authors.affiliation: Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA.
authors.forename: Mete
authors.initials: M
authors.lastname: Civelek
authors.affiliation: Department of Medicine/Division of Cardiology, University of California, Campus - 167917, BH-307 CHS, 10833 Le Conte Ave., Los Angeles, CA, USA.
authors.forename: Calvin
authors.initials: C
authors.lastname: Pan
authors.affiliation: Department of Medicine/Division of Cardiology, University of California, Campus - 167917, BH-307 CHS, 10833 Le Conte Ave., Los Angeles, CA, USA. jlusis@mednet.ucla.edu.
authors.forename: Aldons J
authors.initials: AJ
authors.lastname: Lusis
mesh_terms: D000818:Animals; D001947:Breeding; D003433:Crosses, Genetic; D030561:Databases, Nucleic Acid; D008040:Genetic Linkage; D005828:Genetics, Population / Q000379:methods*; D006801:Humans; D006824:Hybridization, Genetic; D015810:Linkage Disequilibrium; D051379:Mice; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser
keywords: Analysis tools in systems genetics; BxD recombinant inbred strains; GUI-based database analysis suite; Hybrid mouse diversity panel; METSIM in humans; Multilevel population studies