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Integrative Functional Genomics for Systems Genetics in GeneWeaver.org

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Systems Genetics

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

Abstract

The abundance of existing functional genomics studies permits an integrative approach to interpreting and resolving the results of diverse systems genetics studies. However, a major challenge lies in assembling and harmonizing heterogeneous data sets across species for facile comparison to the positional candidate genes and coexpression networks that come from systems genetic studies. GeneWeaver is an online database and suite of tools at www.geneweaver.org that allows for fast aggregation and analysis of gene set-centric data. GeneWeaver contains curated experimental data together with resource-level data such as GO annotations, MP annotations, and KEGG pathways, along with persistent stores of user entered data sets. These can be entered directly into GeneWeaver or transferred from widely used resources such as GeneNetwork.org. Data are analyzed using statistical tools and advanced graph algorithms to discover new relations, prioritize candidate genes, and generate function hypotheses. Here we use GeneWeaver to find genes common to multiple gene sets, prioritize candidate genes from a quantitative trait locus, and characterize a set of differentially expressed genes. Coupling a large multispecies repository curated and empirical functional genomics data to fast computational tools allows for the rapid integrative analysis of heterogeneous data for interpreting and extrapolating systems genetics results.

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Acknowledgements

GeneWeaver is currently supported by NIH AA18776 jointly funded by NIAAA/NIDA.

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Authors and Affiliations

  1. The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA

    Jason A. Bubier & Elissa J. Chesler

  2. Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996, USA

    Michael A. Langston

  3. Institute for Biomedical Studies, Baylor University, Waco, TN, 76798, USA

    Erich J. Baker

Authors
  1. Jason A. Bubier
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  2. Michael A. Langston
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  3. Erich J. Baker
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  4. Elissa J. Chesler
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Corresponding author

Correspondence to Elissa J. Chesler .

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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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Bubier, J.A., Langston, M.A., Baker, E.J., Chesler, E.J. (2017). Integrative Functional Genomics for Systems Genetics in GeneWeaver.org. 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_6

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  • DOI: https://doi.org/10.1007/978-1-4939-6427-7_6

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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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